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Cadmium in PDB 4evd: Crystal Structure Hp-Nap From Strain YS29 Cadmium Loaded (Cocrystallization 50MM)

Protein crystallography data

The structure of Crystal Structure Hp-Nap From Strain YS29 Cadmium Loaded (Cocrystallization 50MM), PDB code: 4evd was solved by H.Yokoyama, O.Tsuruta, N.Akao, S.Fujii, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.65 / 2.20
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 187.412, 187.412, 187.412, 90.00, 90.00, 90.00
R / Rfree (%) 21.3 / 23.7

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure Hp-Nap From Strain YS29 Cadmium Loaded (Cocrystallization 50MM) (pdb code 4evd). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 16 binding sites of Cadmium where determined in the Crystal Structure Hp-Nap From Strain YS29 Cadmium Loaded (Cocrystallization 50MM), PDB code: 4evd:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10; 11; 12; 13; 14; 15; 16;

Cadmium binding site 1 out of 16 in 4evd

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Cadmium binding site 1 out of 16 in the Crystal Structure Hp-Nap From Strain YS29 Cadmium Loaded (Cocrystallization 50MM)


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A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure Hp-Nap From Strain YS29 Cadmium Loaded (Cocrystallization 50MM) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd201

b:20.0
occ:1.00
 NE2 A:HIS25 2.3 15.4 1.0
O A:HOH302 2.5 11.9 1.0
O A:HOH301 2.7 21.8 1.0
CD2 A:HIS25 3.2 16.2 1.0
CE1 A:HIS25 3.3 16.0 1.0
O A:HOH381 3.4 29.8 1.0
O A:HOH303 3.9 21.5 1.0
NE2 A:HIS37 4.1 22.2 1.0
CE1 A:HIS37 4.2 22.3 1.0
OH A:TYR44 4.2 19.6 1.0
CD A:CD202 4.3 23.6 0.5
CG A:HIS25 4.4 17.3 1.0
ND1 A:HIS25 4.4 15.8 1.0
O A:HOH305 4.5 27.0 1.0
NE1 A:TRP26 4.7 17.4 1.0
CD1 A:TRP26 4.8 17.9 1.0
OE1 A:GLU41 4.8 29.6 1.0

Cadmium binding site 2 out of 16 in 4evd

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Cadmium binding site 2 out of 16 in the Crystal Structure Hp-Nap From Strain YS29 Cadmium Loaded (Cocrystallization 50MM)


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A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure Hp-Nap From Strain YS29 Cadmium Loaded (Cocrystallization 50MM) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd202

b:23.6
occ:0.50
 O A:HOH303 2.2 21.5 1.0
O A:HOH301 2.2 21.8 1.0
O A:HOH305 2.4 27.0 1.0
NE2 A:HIS37 2.5 22.2 1.0
O A:HOH304 2.6 39.7 1.0
CD2 A:HIS37 3.0 22.3 1.0
CE1 A:HIS37 3.7 22.3 1.0
O A:HOH381 4.3 29.8 1.0
CD A:CD201 4.3 20.0 1.0
CG A:HIS37 4.3 22.9 1.0
ND1 A:HIS37 4.6 22.6 1.0
CE1 A:HIS25 4.8 16.0 1.0
OE1 A:GLU41 4.9 29.6 1.0
NE2 A:HIS25 4.9 15.4 1.0

Cadmium binding site 3 out of 16 in 4evd

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Cadmium binding site 3 out of 16 in the Crystal Structure Hp-Nap From Strain YS29 Cadmium Loaded (Cocrystallization 50MM)


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A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure Hp-Nap From Strain YS29 Cadmium Loaded (Cocrystallization 50MM) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd203

b:31.3
occ:1.00
 O A:HOH308 2.0 24.2 1.0
O A:HOH306 2.0 17.9 1.0
O A:HOH309 2.3 38.2 1.0
O A:HOH307 2.4 29.2 1.0
ND1 A:HIS101 2.5 20.1 1.0
CE1 A:HIS101 3.4 20.5 1.0
CG A:HIS101 3.5 20.8 1.0
CB A:HIS101 3.8 21.3 1.0
CA A:HIS101 4.1 21.3 1.0
O A:HIS101 4.4 21.2 1.0
OE1 A:GLU105 4.4 26.5 1.0
NE2 A:HIS101 4.5 20.6 1.0
CD2 A:HIS101 4.6 20.3 1.0
C A:HIS101 4.6 21.4 1.0

Cadmium binding site 4 out of 16 in 4evd

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Cadmium binding site 4 out of 16 in the Crystal Structure Hp-Nap From Strain YS29 Cadmium Loaded (Cocrystallization 50MM)


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure Hp-Nap From Strain YS29 Cadmium Loaded (Cocrystallization 50MM) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd204

b:47.5
occ:1.00
 O A:HOH310 2.0 20.2 1.0
OE1 A:GLU94 2.4 27.5 1.0
O A:HOH311 2.5 46.1 1.0
OE2 A:GLU97 2.5 27.6 1.0
OE1 A:GLU97 2.6 27.4 1.0
O A:HOH312 2.7 32.8 1.0
CD A:GLU97 2.9 26.8 1.0
OE2 A:GLU94 3.0 26.1 1.0
CD A:GLU94 3.0 26.2 1.0
CD A:CD215 3.1 42.4 0.2
CG A:GLU97 4.4 24.9 1.0
O A:HOH384 4.4 28.8 1.0
CG A:GLU94 4.5 25.6 1.0
CG A:LYS93 4.7 28.1 1.0
O A:HOH336 4.7 31.3 1.0
CA A:GLU94 4.9 24.6 1.0
O A:HOH376 4.9 42.4 1.0
O A:HOH337 4.9 41.1 1.0
O A:HOH335 4.9 41.9 1.0

Cadmium binding site 5 out of 16 in 4evd

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Cadmium binding site 5 out of 16 in the Crystal Structure Hp-Nap From Strain YS29 Cadmium Loaded (Cocrystallization 50MM)


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Crystal Structure Hp-Nap From Strain YS29 Cadmium Loaded (Cocrystallization 50MM) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd205

b:27.2
occ:0.50
 O A:HOH315 1.8 16.1 1.0
O A:HOH313 1.8 21.4 1.0
OD2 A:ASP53 2.4 17.8 1.0
OD2 A:ASP49 2.4 23.0 1.0
O A:HOH314 2.5 52.5 1.0
OD1 A:ASP49 2.5 22.3 1.0
CG A:ASP49 2.8 20.6 1.0
CG A:ASP53 3.2 17.4 1.0
OD1 A:ASP53 3.3 19.4 1.0
O A:HOH373 3.9 39.8 1.0
O A:HOH383 4.0 43.7 1.0
O A:HOH356 4.2 29.2 1.0
CB A:ASP49 4.3 19.3 1.0
O A:ASP49 4.4 18.9 1.0
CB A:ASP53 4.6 17.2 1.0
C A:ASP49 4.9 18.7 1.0

Cadmium binding site 6 out of 16 in 4evd

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Cadmium binding site 6 out of 16 in the Crystal Structure Hp-Nap From Strain YS29 Cadmium Loaded (Cocrystallization 50MM)


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Crystal Structure Hp-Nap From Strain YS29 Cadmium Loaded (Cocrystallization 50MM) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd206

b:26.2
occ:0.50
 O A:HOH316 2.0 24.1 1.0
O A:HOH317 2.0 44.3 1.0
NE2 A:HIS9 2.4 24.0 1.0
O A:HOH318 2.7 31.6 1.0
CE1 A:HIS9 3.2 23.1 1.0
CD2 A:HIS9 3.4 22.8 1.0
OE2 A:GLU5 3.5 36.6 1.0
ND1 A:HIS9 4.4 22.8 1.0
CG A:HIS9 4.5 22.7 1.0
CD A:GLU5 4.5 35.6 1.0
CB A:GLU5 4.9 29.8 1.0

Cadmium binding site 7 out of 16 in 4evd

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Cadmium binding site 7 out of 16 in the Crystal Structure Hp-Nap From Strain YS29 Cadmium Loaded (Cocrystallization 50MM)


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Crystal Structure Hp-Nap From Strain YS29 Cadmium Loaded (Cocrystallization 50MM) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd207

b:33.5
occ:0.50
 O A:HOH319 2.1 29.9 1.0
O A:HOH320 2.2 52.1 1.0
O A:ALA144 2.4 27.7 1.0
OXT A:ALA144 2.5 27.6 1.0
C A:ALA144 2.8 27.4 1.0
O A:HOH359 4.0 25.4 1.0
CA A:ALA144 4.3 27.1 1.0

Cadmium binding site 8 out of 16 in 4evd

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Cadmium binding site 8 out of 16 in the Crystal Structure Hp-Nap From Strain YS29 Cadmium Loaded (Cocrystallization 50MM)


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Crystal Structure Hp-Nap From Strain YS29 Cadmium Loaded (Cocrystallization 50MM) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd208

b:30.4
occ:0.50
 O A:HOH322 1.8 24.2 1.0
O A:HOH321 2.0 40.6 1.0
OE2 A:GLU45 2.5 24.5 1.0
OE1 A:GLU45 2.5 25.3 1.0
OE2 A:GLU42 2.6 29.2 1.0
CD A:GLU45 2.8 23.8 1.0
OE2 A:GLU41 2.9 29.5 1.0
CD A:GLU42 3.4 27.4 1.0
OE1 A:GLU42 3.6 29.6 1.0
CD A:GLU41 3.9 27.6 1.0
CG A:GLU41 4.1 24.2 1.0
CG A:GLU45 4.3 21.6 1.0
O A:HOH368 4.8 36.8 1.0
CG A:GLU42 4.8 23.4 1.0

Cadmium binding site 9 out of 16 in 4evd

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Cadmium binding site 9 out of 16 in the Crystal Structure Hp-Nap From Strain YS29 Cadmium Loaded (Cocrystallization 50MM)


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Crystal Structure Hp-Nap From Strain YS29 Cadmium Loaded (Cocrystallization 50MM) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd209

b:25.4
occ:0.50
 O A:HOH323 1.8 38.3 1.0
O A:HOH324 1.9 33.5 1.0
OE1 A:GLU108 2.1 31.2 1.0
O A:HOH325 2.2 26.2 1.0
OE1 A:GLU105 2.5 26.5 1.0
OE2 A:GLU105 2.7 27.2 1.0
CD A:GLU105 2.9 27.0 1.0
CD A:GLU108 2.9 31.3 1.0
OE2 A:GLU108 3.1 32.4 1.0
NH1 A:ARG77 4.3 31.5 1.0
CG A:GLU108 4.3 28.6 1.0
CG A:GLU105 4.4 25.8 1.0
CB A:GLU108 4.7 26.7 1.0
O A:HOH385 4.8 28.1 1.0
NH2 A:ARG77 4.9 31.4 1.0
CA A:GLU105 4.9 25.2 1.0

Cadmium binding site 10 out of 16 in 4evd

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Cadmium binding site 10 out of 16 in the Crystal Structure Hp-Nap From Strain YS29 Cadmium Loaded (Cocrystallization 50MM)


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A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Crystal Structure Hp-Nap From Strain YS29 Cadmium Loaded (Cocrystallization 50MM) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd210

b:43.8
occ:0.50
 O A:HOH328 2.1 42.5 1.0
O A:HOH327 2.2 36.4 1.0
O A:HOH326 2.3 29.7 1.0
OD2 A:ASP90 2.5 27.6 1.0
ND1 A:HIS87 2.9 28.8 1.0
CG A:ASP90 3.4 26.3 1.0
OD1 A:ASP90 3.5 27.6 1.0
CG A:HIS87 3.6 27.9 1.0
CB A:HIS87 3.6 26.7 1.0
N A:HIS87 3.8 26.0 1.0
CE1 A:HIS87 3.9 29.0 1.0
CA A:HIS87 4.3 26.4 1.0
C A:PHE86 4.7 25.8 1.0
CB A:ASP90 4.8 25.2 1.0
CD2 A:HIS87 4.8 28.6 1.0
NE2 A:HIS87 4.9 29.2 1.0
CA A:PHE86 4.9 25.6 1.0

Cadmium binding site 11 out of 16 in 4evd

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Cadmium binding site 11 out of 16 in the Crystal Structure Hp-Nap From Strain YS29 Cadmium Loaded (Cocrystallization 50MM)


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 11 of Crystal Structure Hp-Nap From Strain YS29 Cadmium Loaded (Cocrystallization 50MM) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd211

b:29.3
occ:0.25
 ND1 A:HIS63 2.3 30.1 1.0
O A:HOH329 2.5 33.6 1.0
CE1 A:HIS63 3.1 31.0 1.0
CG A:HIS63 3.4 28.8 1.0
CB A:HIS63 3.9 26.8 1.0
CA A:HIS63 4.2 26.5 1.0
NE2 A:HIS63 4.3 31.1 1.0
CD2 A:HIS63 4.5 29.9 1.0
CE1 A:PHE4 4.7 31.4 1.0
CZ A:PHE4 4.8 31.8 1.0
N A:HIS64 4.8 25.8 1.0
O A:GLY62 4.9 26.3 1.0

Cadmium binding site 12 out of 16 in 4evd

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Cadmium binding site 12 out of 16 in the Crystal Structure Hp-Nap From Strain YS29 Cadmium Loaded (Cocrystallization 50MM)


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 12 of Crystal Structure Hp-Nap From Strain YS29 Cadmium Loaded (Cocrystallization 50MM) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd212

b:42.8
occ:0.25
 O A:HOH331 1.8 41.4 1.0
O A:HOH330 2.0 34.5 1.0
NE2 A:HIS63 2.5 31.1 1.0
CE1 A:HIS63 3.0 31.0 1.0
CD2 A:HIS63 3.6 29.9 1.0
O A:HOH380 4.2 38.2 1.0
ND1 A:HIS63 4.3 30.1 1.0
CE A:LYS2 4.3 34.6 1.0
O A:LEU61 4.5 25.5 1.0
CG A:HIS63 4.6 28.8 1.0
NZ A:LYS2 4.8 34.0 1.0

Cadmium binding site 13 out of 16 in 4evd

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Cadmium binding site 13 out of 16 in the Crystal Structure Hp-Nap From Strain YS29 Cadmium Loaded (Cocrystallization 50MM)


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 13 of Crystal Structure Hp-Nap From Strain YS29 Cadmium Loaded (Cocrystallization 50MM) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd213

b:43.5
occ:0.25
 O A:HOH334 1.9 34.3 1.0
O A:HOH332 2.2 48.0 1.0
O A:HOH333 2.3 46.7 1.0
NE2 A:HIS64 2.7 30.0 1.0
CD2 A:HIS64 3.5 29.1 1.0
CE1 A:HIS64 3.7 29.6 1.0
CD A:CD214 4.6 26.6 0.2
CG A:HIS64 4.7 27.9 1.0
ND1 A:HIS64 4.8 29.2 1.0

Cadmium binding site 14 out of 16 in 4evd

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Cadmium binding site 14 out of 16 in the Crystal Structure Hp-Nap From Strain YS29 Cadmium Loaded (Cocrystallization 50MM)


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 14 of Crystal Structure Hp-Nap From Strain YS29 Cadmium Loaded (Cocrystallization 50MM) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd214

b:26.6
occ:0.25
 O A:HOH332 2.6 48.0 1.0
CE1 A:HIS64 2.8 29.6 1.0
NE2 A:HIS64 3.6 30.0 1.0
ND1 A:HIS64 3.8 29.2 1.0
O A:HOH333 4.5 46.7 1.0
CD A:CD213 4.6 43.5 0.2
CD2 A:HIS64 4.9 29.1 1.0
CG A:HIS64 4.9 27.9 1.0

Cadmium binding site 15 out of 16 in 4evd

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Cadmium binding site 15 out of 16 in the Crystal Structure Hp-Nap From Strain YS29 Cadmium Loaded (Cocrystallization 50MM)


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 15 of Crystal Structure Hp-Nap From Strain YS29 Cadmium Loaded (Cocrystallization 50MM) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd215

b:42.4
occ:0.25
 O A:HOH310 2.0 20.2 1.0
O A:HOH337 2.2 41.1 1.0
O A:HOH336 2.3 31.3 1.0
OE2 A:GLU97 2.4 27.6 1.0
O A:HOH335 2.4 41.9 1.0
OE2 A:GLU94 2.5 26.1 1.0
CD A:CD204 3.1 47.5 1.0
CD A:GLU97 3.6 26.8 1.0
CD A:GLU94 3.6 26.2 1.0
O A:HOH343 3.9 24.3 1.0
O A:HOH311 4.0 46.1 1.0
OE1 A:GLU94 4.1 27.5 1.0
CB A:GLU97 4.4 23.2 1.0
OE1 A:GLU97 4.4 27.4 1.0
CG A:GLU97 4.6 24.9 1.0
NZ A:LYS20 4.7 19.4 1.0
CG A:GLU94 4.8 25.6 1.0
CA A:GLU94 4.8 24.6 1.0
O A:GLU94 4.9 24.0 1.0
CB A:GLU94 5.0 24.8 1.0
OD1 A:ASP98 5.0 23.3 1.0

Cadmium binding site 16 out of 16 in 4evd

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Cadmium binding site 16 out of 16 in the Crystal Structure Hp-Nap From Strain YS29 Cadmium Loaded (Cocrystallization 50MM)


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 16 of Crystal Structure Hp-Nap From Strain YS29 Cadmium Loaded (Cocrystallization 50MM) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd216

b:44.0
occ:0.50
 O A:HOH338 2.1 47.3 1.0
OE1 A:GLU46 2.4 27.1 1.0
OE2 A:GLU46 2.6 28.0 1.0
CD A:GLU46 2.8 26.2 1.0
O A:HOH365 3.3 45.0 1.0
OG A:SER135 4.3 21.8 1.0
CG A:GLU46 4.4 23.4 1.0
O A:HOH367 4.5 24.1 1.0
O A:HOH379 4.6 25.6 1.0
CG1 A:ILE43 4.8 18.7 1.0

Reference:

H.Yokoyama, O.Tsuruta, N.Akao, S.Fujii. Crystal Structure of Helicobacter Pylori Neutrophil-Activating Protein with A Di-Nuclear Ferroxidase Center in A Zinc or Cadmium-Bound Form Biochem.Biophys.Res.Commun. V. 422 745 2012.
ISSN: ISSN 0006-291X
PubMed: 22618234
DOI: 10.1016/J.BBRC.2012.05.073
Page generated: Fri Aug 28 14:26:42 2020
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