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Cadmium in PDB 4qq2: Crystal Structure of C1QL1

Protein crystallography data

The structure of Crystal Structure of C1QL1, PDB code: 4qq2 was solved by S.Ressl, A.T.Brunger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.17 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 53.072, 71.414, 85.972, 90.00, 90.00, 90.00
R / Rfree (%) 16.5 / 20

Cadmium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Cadmium atom in the Crystal Structure of C1QL1 (pdb code 4qq2). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 18 binding sites of Cadmium where determined in the Crystal Structure of C1QL1, PDB code: 4qq2:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 18 in 4qq2

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Cadmium binding site 1 out of 18 in the Crystal Structure of C1QL1


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of C1QL1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd201

b:12.7
occ:1.00
OD2 B:ASP89 2.4 8.7 1.0
OD2 C:ASP89 2.4 9.8 1.0
OD2 A:ASP89 2.5 14.4 1.0
O B:HOH386 2.6 19.5 1.0
O C:HOH328 2.6 29.8 1.0
OD1 C:ASP89 2.8 13.3 1.0
O C:HOH364 2.9 43.4 1.0
CG C:ASP89 2.9 15.9 1.0
OD1 A:ASP89 3.0 12.8 1.0
CG A:ASP89 3.1 10.4 1.0
CG B:ASP89 3.2 13.7 1.0
OD1 B:ASP89 3.2 14.2 1.0
O B:HOH345 4.3 9.9 1.0
O C:HOH309 4.4 7.7 1.0
CB C:ASP89 4.4 9.4 1.0
O A:HOH325 4.5 9.1 1.0
CB A:ASP89 4.5 8.4 1.0
CB B:ASP89 4.6 8.6 1.0

Cadmium binding site 2 out of 18 in 4qq2

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Cadmium binding site 2 out of 18 in the Crystal Structure of C1QL1


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of C1QL1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd202

b:6.9
occ:1.00
OD2 A:ASP93 2.3 5.3 1.0
OD2 C:ASP93 2.4 5.7 1.0
OD2 B:ASP93 2.4 9.1 1.0
O A:HOH332 2.4 6.3 1.0
O B:HOH340 2.5 9.2 1.0
O C:HOH301 2.5 4.0 1.0
CG A:ASP93 3.3 9.7 1.0
CG C:ASP93 3.3 7.5 1.0
CG B:ASP93 3.3 6.5 1.0
OD1 A:ASP93 3.8 5.2 1.0
OD1 B:ASP93 3.9 6.2 1.0
OD1 C:ASP93 3.9 5.7 1.0
OD1 B:ASP87 4.1 6.2 1.0
CD A:CD203 4.1 6.5 1.0
OD1 C:ASP87 4.1 8.9 1.0
OD1 A:ASP87 4.2 6.6 1.0
O A:HOH306 4.3 6.0 1.0
O C:HOH305 4.3 3.4 1.0
O B:HOH314 4.3 5.3 1.0
CB A:ASP93 4.3 5.4 1.0
CB B:ASP93 4.3 5.5 1.0
CB C:ASP93 4.4 6.5 1.0
O A:GLN86 4.5 5.8 1.0
O C:GLN86 4.5 6.1 1.0
O B:GLN86 4.5 5.3 1.0

Cadmium binding site 3 out of 18 in 4qq2

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Cadmium binding site 3 out of 18 in the Crystal Structure of C1QL1


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of C1QL1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd203

b:6.5
occ:1.00
OD1 A:ASP93 2.4 5.2 1.0
OD1 C:ASP93 2.4 5.7 1.0
OD1 B:ASP93 2.4 6.2 1.0
O B:HOH302 2.5 5.1 1.0
O C:HOH303 2.5 4.8 1.0
O A:HOH312 2.5 5.3 1.0
CG A:ASP93 3.3 9.7 1.0
CG C:ASP93 3.3 7.5 1.0
CG B:ASP93 3.3 6.5 1.0
OD2 B:ASP93 3.4 9.1 1.0
OD2 A:ASP93 3.4 5.3 1.0
OD2 C:ASP93 3.4 5.7 1.0
CD A:CD202 4.1 6.9 1.0
O C:HOH312 4.2 5.3 1.0
O B:HOH303 4.2 5.0 1.0
O A:HOH386 4.3 26.8 1.0
O A:HOH308 4.3 7.9 1.0
O C:HOH411 4.5 38.7 1.0
O A:HOH387 4.5 30.8 1.0
N C:TYR94 4.5 5.8 1.0
N B:TYR94 4.5 5.8 1.0
N A:TYR94 4.6 8.9 1.0
O A:HOH306 4.6 6.0 1.0
O B:HOH314 4.6 5.3 1.0
O C:HOH305 4.7 3.4 1.0
CB A:ASP93 4.7 5.4 1.0
CB B:ASP93 4.7 5.5 1.0
CB C:ASP93 4.7 6.5 1.0
O C:TYR94 4.8 6.6 1.0
O B:TYR94 4.8 6.1 1.0
O A:TYR94 4.9 5.2 1.0

Cadmium binding site 4 out of 18 in 4qq2

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Cadmium binding site 4 out of 18 in the Crystal Structure of C1QL1


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of C1QL1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd204

b:14.6
occ:1.00
O A:HOH342 2.4 10.5 1.0
OE2 A:GLU20 2.4 12.0 1.0
OE1 A:GLU20 2.5 13.6 1.0
O A:HOH310 2.5 10.1 1.0
CD A:GLU20 2.8 12.2 1.0
O A:HOH366 2.8 24.0 1.0
NZ A:LYS117 3.8 13.5 0.9
CG A:GLU20 4.3 10.6 1.0
NH1 A:ARG62 4.3 13.9 1.0
O A:HOH395 4.3 37.9 1.0
NH1 A:ARG62 4.4 12.8 0.0
O A:HOH329 4.5 32.0 1.0
O A:HOH381 4.5 23.9 1.0
NZ A:LYS117 4.6 9.8 0.1
CE A:LYS117 4.7 9.7 0.1
O A:HOH324 4.7 16.1 1.0
O A:HOH316 4.8 13.5 1.0
CE A:LYS117 4.9 10.9 0.9
O A:HOH421 5.0 43.6 1.0

Cadmium binding site 5 out of 18 in 4qq2

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Cadmium binding site 5 out of 18 in the Crystal Structure of C1QL1


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Crystal Structure of C1QL1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd205

b:10.5
occ:1.00
OD2 A:ASP72 2.4 10.8 1.0
OD2 A:ASP114 2.4 8.0 1.0
O A:HOH360 2.5 9.7 1.0
O A:HOH359 2.5 5.8 1.0
O A:HOH347 2.5 14.0 1.0
O A:HOH361 2.5 9.3 1.0
CG A:ASP72 3.2 10.8 1.0
OD1 A:ASP72 3.4 10.4 1.0
CG A:ASP114 3.5 10.9 1.0
CB A:ASP114 3.9 9.2 1.0
O A:HOH337 4.2 14.0 1.0
O A:HOH424 4.2 13.8 1.0
OH C:TYR126 4.4 10.8 1.0
CD A:CD206 4.4 14.0 1.0
O A:HOH415 4.5 5.6 1.0
OG A:SER82 4.5 7.7 1.0
O C:HOH390 4.5 29.7 1.0
CB A:ASP72 4.6 7.5 1.0
O A:HOH436 4.6 21.6 1.0
OD1 A:ASP114 4.6 12.4 1.0
O C:HOH316 4.6 23.4 1.0
O A:HOH355 4.8 27.3 1.0
CG2 A:VAL79 4.9 11.4 1.0
OD1 C:ASN124 5.0 25.0 1.0

Cadmium binding site 6 out of 18 in 4qq2

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Cadmium binding site 6 out of 18 in the Crystal Structure of C1QL1


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Crystal Structure of C1QL1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd206

b:14.0
occ:1.00
OD1 A:ASP114 2.4 12.4 1.0
OD2 A:ASP114 2.5 8.0 1.0
O A:HOH415 2.5 5.6 1.0
O A:HOH355 2.6 27.3 1.0
O A:HOH436 2.7 21.6 1.0
CG A:ASP114 2.8 10.9 1.0
O A:HOH347 4.0 14.0 1.0
O A:HOH427 4.2 21.4 1.0
O A:HOH361 4.2 9.3 1.0
CB A:ASP114 4.3 9.2 1.0
O A:HOH337 4.3 14.0 1.0
CD A:CD205 4.4 10.5 1.0
CE2 A:TYR22 4.5 9.9 1.0
O A:ASP114 4.5 7.2 1.0
O A:HOH340 4.6 29.7 1.0
CD2 A:TYR22 4.8 11.5 1.0
CA A:ASP114 5.0 7.3 1.0

Cadmium binding site 7 out of 18 in 4qq2

Go back to Cadmium Binding Sites List in 4qq2
Cadmium binding site 7 out of 18 in the Crystal Structure of C1QL1


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Crystal Structure of C1QL1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd207

b:13.2
occ:1.00
ND1 A:HIS119 2.4 9.4 1.0
O A:HOH434 2.5 1.3 1.0
O A:HOH432 2.5 1.3 1.0
O A:HOH358 2.5 5.3 1.0
CE1 A:HIS119 3.3 11.5 1.0
CG A:HIS119 3.4 7.7 1.0
CB A:HIS119 3.7 6.8 1.0
CA A:HIS119 4.1 6.9 1.0
O A:HOH384 4.2 23.1 1.0
O A:GLY120 4.4 9.6 1.0
NE2 A:HIS119 4.5 8.7 1.0
O A:HOH400 4.5 37.5 1.0
CD2 A:HIS119 4.5 7.5 1.0
O A:HOH409 4.6 30.0 1.0
N A:GLY120 4.7 8.0 1.0
CG A:ARG62 4.7 9.4 0.0
CG A:ARG62 4.8 10.5 1.0
C A:HIS119 4.9 8.0 1.0

Cadmium binding site 8 out of 18 in 4qq2

Go back to Cadmium Binding Sites List in 4qq2
Cadmium binding site 8 out of 18 in the Crystal Structure of C1QL1


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Crystal Structure of C1QL1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd208

b:13.8
occ:1.00
O A:HOH431 2.5 1.3 1.0
O A:HOH392 2.6 4.6 1.0
CG2 A:VAL24 4.1 9.1 1.0
O A:HOH350 4.4 30.2 1.0
N A:VAL24 4.5 8.6 1.0
CB A:VAL24 4.6 11.3 1.0
NZ A:LYS26 4.8 24.5 1.0

Cadmium binding site 9 out of 18 in 4qq2

Go back to Cadmium Binding Sites List in 4qq2
Cadmium binding site 9 out of 18 in the Crystal Structure of C1QL1


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Crystal Structure of C1QL1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd209

b:39.8
occ:1.00
O A:HOH394 2.7 12.4 1.0
O A:HOH433 3.6 1.3 1.0
ND2 A:ASN76 4.6 14.4 1.0
OD1 A:ASP107 4.7 14.0 1.0

Cadmium binding site 10 out of 18 in 4qq2

Go back to Cadmium Binding Sites List in 4qq2
Cadmium binding site 10 out of 18 in the Crystal Structure of C1QL1


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Crystal Structure of C1QL1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd201

b:8.6
occ:1.00
OD1 B:ASP87 2.4 6.2 1.0
OD1 A:ASP87 2.4 6.6 1.0
OD1 C:ASP87 2.4 8.9 1.0
O C:HOH309 2.4 7.7 1.0
O B:HOH345 2.5 9.9 1.0
O A:HOH325 2.5 9.1 1.0
CG B:ASP87 3.2 9.8 1.0
CG C:ASP87 3.2 8.1 1.0
CG A:ASP87 3.2 7.7 1.0
OD2 B:ASP87 3.5 6.8 1.0
OD2 C:ASP87 3.5 7.7 1.0
OD2 A:ASP87 3.6 7.1 1.0
OD2 C:ASP89 4.1 9.8 1.0
O A:HOH332 4.1 6.3 1.0
OD2 A:ASP89 4.2 14.4 1.0
O B:HOH340 4.3 9.2 1.0
O C:HOH301 4.3 4.0 1.0
OD1 A:ASN91 4.3 20.1 1.0
OD2 B:ASP89 4.3 8.7 1.0
CB B:ASP87 4.4 7.3 1.0
OD1 B:ASN91 4.4 14.9 1.0
OD1 C:ASN91 4.4 14.0 1.0
CB A:ASP87 4.4 6.4 1.0
CB C:ASP87 4.5 6.7 1.0
CA B:ASP87 4.7 5.8 1.0
CA A:ASP87 4.8 6.5 1.0
CA C:ASP87 4.8 8.2 1.0
CG C:ASP89 4.9 15.9 1.0
N B:ALA88 4.9 8.0 1.0
N A:ALA88 4.9 7.7 1.0

Reference:

S.Ressl, B.K.Vu, S.Vivona, D.C.Martinelli, T.C.Sudhof, A.T.Brunger. Structures of C1Q-Like Proteins Reveal Unique Features Among the C1Q/Tnf Superfamily. Structure V. 23 688 2015.
ISSN: ISSN 0969-2126
PubMed: 25752542
DOI: 10.1016/J.STR.2015.01.019
Page generated: Sat Dec 12 08:25:43 2020

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