Atomistry » Cadmium » PDB 4evc-4l1l » 4evd
Atomistry »
  Cadmium »
    PDB 4evc-4l1l »
      4evd »

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:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

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;

Cadmium binding site 1 out of 16 in 4evd

Go back to Cadmium Binding Sites List in 4evd
Cadmium binding site 1 out of 16 in the Crystal Structure Hp-Nap From Strain YS29 Cadmium Loaded (Cocrystallization 50MM)


Mono view


Stereo pair view

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

Go back to Cadmium Binding Sites List in 4evd
Cadmium binding site 2 out of 16 in the Crystal Structure Hp-Nap From Strain YS29 Cadmium Loaded (Cocrystallization 50MM)


Mono view


Stereo pair view

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

Go back to Cadmium Binding Sites List in 4evd
Cadmium binding site 3 out of 16 in the Crystal Structure Hp-Nap From Strain YS29 Cadmium Loaded (Cocrystallization 50MM)


Mono view


Stereo pair view

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

Go back to Cadmium Binding Sites List in 4evd
Cadmium binding site 4 out of 16 in the Crystal Structure Hp-Nap From Strain YS29 Cadmium Loaded (Cocrystallization 50MM)


Mono view


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

Go back to Cadmium Binding Sites List in 4evd
Cadmium binding site 5 out of 16 in the Crystal Structure Hp-Nap From Strain YS29 Cadmium Loaded (Cocrystallization 50MM)


Mono view


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

Go back to Cadmium Binding Sites List in 4evd
Cadmium binding site 6 out of 16 in the Crystal Structure Hp-Nap From Strain YS29 Cadmium Loaded (Cocrystallization 50MM)


Mono view


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

Go back to Cadmium Binding Sites List in 4evd
Cadmium binding site 7 out of 16 in the Crystal Structure Hp-Nap From Strain YS29 Cadmium Loaded (Cocrystallization 50MM)


Mono view


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

Go back to Cadmium Binding Sites List in 4evd
Cadmium binding site 8 out of 16 in the Crystal Structure Hp-Nap From Strain YS29 Cadmium Loaded (Cocrystallization 50MM)


Mono view


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

Go back to Cadmium Binding Sites List in 4evd
Cadmium binding site 9 out of 16 in the Crystal Structure Hp-Nap From Strain YS29 Cadmium Loaded (Cocrystallization 50MM)


Mono view


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

Go back to Cadmium Binding Sites List in 4evd
Cadmium binding site 10 out of 16 in the Crystal Structure Hp-Nap From Strain YS29 Cadmium Loaded (Cocrystallization 50MM)


Mono view


Stereo pair view

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

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: Thu Jul 10 13:32:27 2025

Last articles

Cl in 2Q5L
Cl in 2Q3L
Cl in 2Q3G
Cl in 2Q3I
Cl in 2Q3B
Cl in 2Q02
Cl in 2Q2F
Cl in 2Q35
Cl in 2Q22
Cl in 2Q14
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy