Atomistry » Cadmium » PDB 6w8a-7kgq » 7d30
Atomistry »
  Cadmium »
    PDB 6w8a-7kgq »
      7d30 »

Cadmium in PDB 7d30: Structure of Sybody MR17-SR31 Fusion in Complex with the Sars-Cov-2 S Receptor Binding Domain (Rbd)

Protein crystallography data

The structure of Structure of Sybody MR17-SR31 Fusion in Complex with the Sars-Cov-2 S Receptor Binding Domain (Rbd), PDB code: 7d30 was solved by T.Li, H.Yao, H.Cai, W.Qin, D.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.70 / 2.10
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 73.384, 73.384, 478.363, 90, 90, 120
R / Rfree (%) 19.5 / 23.6

Cadmium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 17;

Binding sites:

The binding sites of Cadmium atom in the Structure of Sybody MR17-SR31 Fusion in Complex with the Sars-Cov-2 S Receptor Binding Domain (Rbd) (pdb code 7d30). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 17 binding sites of Cadmium where determined in the Structure of Sybody MR17-SR31 Fusion in Complex with the Sars-Cov-2 S Receptor Binding Domain (Rbd), PDB code: 7d30:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 17 in 7d30

Go back to Cadmium Binding Sites List in 7d30
Cadmium binding site 1 out of 17 in the Structure of Sybody MR17-SR31 Fusion in Complex with the Sars-Cov-2 S Receptor Binding Domain (Rbd)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Structure of Sybody MR17-SR31 Fusion in Complex with the Sars-Cov-2 S Receptor Binding Domain (Rbd) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1314

b:69.2
occ:0.50
OXT B:ACT2104 2.2 84.8 1.0
OXT A:ACT1302 2.2 88.0 1.0
O A:ACT1302 2.2 87.3 1.0
OD2 A:ASP1062 2.2 81.5 1.0
OXT B:GLN539 2.2 99.0 1.0
O B:GLN539 2.2 93.8 1.0
OD1 A:ASP1062 2.3 72.6 1.0
C A:ACT1302 2.4 95.6 1.0
C B:GLN539 2.6 95.9 1.0
CG A:ASP1062 2.6 69.5 1.0
C B:ACT2104 2.9 94.5 1.0
O B:ACT2104 3.2 95.4 1.0
NZ A:LYS1065 3.9 68.3 1.0
CH3 A:ACT1302 4.0 85.2 1.0
CA B:GLN539 4.1 104.6 1.0
CB A:ASP1062 4.1 61.4 1.0
CH3 B:ACT2104 4.4 92.9 1.0
N B:GLN539 4.8 100.4 1.0
CB B:GLN539 4.8 103.0 1.0

Cadmium binding site 2 out of 17 in 7d30

Go back to Cadmium Binding Sites List in 7d30
Cadmium binding site 2 out of 17 in the Structure of Sybody MR17-SR31 Fusion in Complex with the Sars-Cov-2 S Receptor Binding Domain (Rbd)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Structure of Sybody MR17-SR31 Fusion in Complex with the Sars-Cov-2 S Receptor Binding Domain (Rbd) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1315

b:129.7
occ:0.48
O A:HOH1487 2.2 67.6 1.0
O A:HOH1505 2.2 85.8 1.0
OE2 A:GLU89 2.3 64.2 1.0
CD A:GLU89 3.2 71.7 1.0
OE1 A:GLU89 3.5 89.1 1.0
CD A:PRO88 3.8 56.1 1.0
CG A:PRO88 4.2 50.5 1.0
CG A:GLU89 4.6 66.3 1.0
CB A:PRO88 4.7 54.9 1.0
N A:PRO88 4.7 57.6 1.0
CB A:LYS87 4.7 55.6 1.0
N A:GLU89 5.0 39.7 1.0

Cadmium binding site 3 out of 17 in 7d30

Go back to Cadmium Binding Sites List in 7d30
Cadmium binding site 3 out of 17 in the Structure of Sybody MR17-SR31 Fusion in Complex with the Sars-Cov-2 S Receptor Binding Domain (Rbd)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Structure of Sybody MR17-SR31 Fusion in Complex with the Sars-Cov-2 S Receptor Binding Domain (Rbd) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1316

b:107.3
occ:0.56
SD A:MET1054 3.3 70.3 1.0
CG A:MET1054 4.6 62.7 1.0
CE A:MET1054 4.7 73.8 1.0
NE1 A:TRP1030 4.8 62.7 1.0
CB A:MET1054 4.9 52.9 1.0

Cadmium binding site 4 out of 17 in 7d30

Go back to Cadmium Binding Sites List in 7d30
Cadmium binding site 4 out of 17 in the Structure of Sybody MR17-SR31 Fusion in Complex with the Sars-Cov-2 S Receptor Binding Domain (Rbd)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Structure of Sybody MR17-SR31 Fusion in Complex with the Sars-Cov-2 S Receptor Binding Domain (Rbd) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1317

b:150.8
occ:0.60
O A:HOH1468 2.2 34.5 1.0
O A:HOH1471 2.3 54.5 1.0
CD A:CD1323 3.3 123.5 0.3
CD A:CD1324 3.7 39.8 0.7
CE A:LYS99 3.8 69.0 1.0
O A:VAL98 3.9 42.8 1.0
OD2 A:ASP109 4.1 53.3 1.0
ND2 A:ASN97 4.3 41.2 1.0
CA A:LYS99 4.4 36.6 1.0
NZ A:LYS99 4.4 75.6 1.0
CG A:ASP109 4.4 64.7 1.0
OD1 A:ASP100 4.5 35.1 1.0
CD A:LYS99 4.6 60.2 1.0
OD1 A:ASP109 4.6 71.7 1.0
O A:HOH1478 4.7 57.0 1.0
N A:ASP100 4.7 38.6 1.0
OD1 A:ASN97 4.7 51.6 1.0
N A:ASP101 4.8 39.5 1.0
C A:VAL98 4.8 37.3 1.0
C A:LYS99 4.9 37.9 1.0
CG A:LYS99 5.0 55.8 1.0

Cadmium binding site 5 out of 17 in 7d30

Go back to Cadmium Binding Sites List in 7d30
Cadmium binding site 5 out of 17 in the Structure of Sybody MR17-SR31 Fusion in Complex with the Sars-Cov-2 S Receptor Binding Domain (Rbd)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Structure of Sybody MR17-SR31 Fusion in Complex with the Sars-Cov-2 S Receptor Binding Domain (Rbd) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1318

b:129.1
occ:0.32
OXT A:ACT1303 2.2 95.0 1.0
OE1 A:GLU1089 2.2 96.7 1.0
O A:ACT1303 2.2 114.6 1.0
OE2 A:GLU1089 2.2 74.6 1.0
CD A:GLU1089 2.4 81.4 1.0
C A:ACT1303 2.4 94.6 1.0
CG A:GLU1089 3.7 81.3 1.0
CH3 A:ACT1303 4.0 84.9 1.0
O A:HOH1496 4.1 78.7 1.0
CD A:PRO1088 4.8 61.8 1.0
CG A:LYS1087 4.9 74.9 1.0
CB A:LYS1087 4.9 65.5 1.0
CB A:GLU1089 4.9 62.3 1.0
CD A:LYS1087 4.9 75.0 1.0

Cadmium binding site 6 out of 17 in 7d30

Go back to Cadmium Binding Sites List in 7d30
Cadmium binding site 6 out of 17 in the Structure of Sybody MR17-SR31 Fusion in Complex with the Sars-Cov-2 S Receptor Binding Domain (Rbd)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Structure of Sybody MR17-SR31 Fusion in Complex with the Sars-Cov-2 S Receptor Binding Domain (Rbd) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1319

b:103.0
occ:0.39
OXT A:ACT1306 2.2 99.9 1.0
O A:ACT1306 2.2 96.6 1.0
O A:ACT1307 2.2 92.0 1.0
OXT A:ACT1307 2.2 64.8 1.0
C A:ACT1307 2.4 84.6 1.0
C A:ACT1306 2.4 91.2 1.0
O A:ASN74 3.7 46.8 1.0
CH3 A:ACT1307 3.8 48.6 1.0
CH3 A:ACT1306 4.0 64.1 1.0
O A:HOH1404 4.0 76.2 1.0
OE2 A:GLU30 4.2 58.7 1.0
C A:ASN74 4.3 46.4 1.0
OE1 A:GLU30 4.3 47.2 1.0
CB A:ASN74 4.6 51.2 1.0
CD A:GLU30 4.7 56.6 1.0
CA A:ASN74 4.9 46.9 1.0
N A:ALA75 4.9 45.6 1.0
OD1 A:ASN77 4.9 41.5 1.0

Cadmium binding site 7 out of 17 in 7d30

Go back to Cadmium Binding Sites List in 7d30
Cadmium binding site 7 out of 17 in the Structure of Sybody MR17-SR31 Fusion in Complex with the Sars-Cov-2 S Receptor Binding Domain (Rbd)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Structure of Sybody MR17-SR31 Fusion in Complex with the Sars-Cov-2 S Receptor Binding Domain (Rbd) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1320

b:143.3
occ:0.61
OD2 A:ASP62 2.2 104.6 1.0
CG A:ASP62 3.2 83.1 1.0
OD1 A:ASP62 3.4 83.8 1.0
CG2 B:THR478 3.6 83.7 1.0
CB A:ASP62 4.5 63.9 1.0
CB B:GLU484 4.8 76.3 1.0
CB B:THR478 5.0 84.0 1.0

Cadmium binding site 8 out of 17 in 7d30

Go back to Cadmium Binding Sites List in 7d30
Cadmium binding site 8 out of 17 in the Structure of Sybody MR17-SR31 Fusion in Complex with the Sars-Cov-2 S Receptor Binding Domain (Rbd)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Structure of Sybody MR17-SR31 Fusion in Complex with the Sars-Cov-2 S Receptor Binding Domain (Rbd) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1321

b:135.2
occ:0.50
OE2 A:GLU46 2.9 64.0 1.0
O A:HOH1497 2.9 80.6 1.0
OE1 A:GLU46 3.2 56.0 1.0
CD A:GLU46 3.4 63.1 1.0
OG A:SER63 3.8 54.2 1.0
CB A:SER63 4.0 50.1 1.0
NH2 A:ARG38 4.2 41.8 1.0
O A:HOH1467 4.2 53.5 1.0
O A:HOH1405 4.4 52.5 1.0
CG A:GLU46 4.8 57.0 1.0

Cadmium binding site 9 out of 17 in 7d30

Go back to Cadmium Binding Sites List in 7d30
Cadmium binding site 9 out of 17 in the Structure of Sybody MR17-SR31 Fusion in Complex with the Sars-Cov-2 S Receptor Binding Domain (Rbd)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Structure of Sybody MR17-SR31 Fusion in Complex with the Sars-Cov-2 S Receptor Binding Domain (Rbd) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1322

b:107.0
occ:0.49
O A:HOH1443 2.3 53.2 1.0
O A:PHE68 3.0 43.1 1.0
N A:GLY66 3.5 56.4 1.0
CA A:GLY66 4.1 53.1 1.0
CE2 A:TYR60 4.1 42.1 1.0
CZ A:TYR60 4.1 34.9 1.0
C A:PHE68 4.2 40.5 1.0
CD2 A:TYR60 4.3 42.3 1.0
OG1 A:THR69 4.3 42.5 1.0
CE1 A:TYR60 4.4 34.9 1.0
CG A:TYR60 4.5 38.0 1.0
C A:GLY66 4.5 51.3 1.0
CD1 A:TYR60 4.5 31.6 1.0
N A:ARG67 4.6 43.2 1.0
C A:LYS65 4.6 52.5 1.0
OH A:TYR60 4.6 38.4 1.0
N A:PHE68 4.7 43.1 1.0
CA A:LYS65 4.7 52.0 0.6
CA A:LYS65 4.7 52.0 0.5
O A:VAL64 4.9 42.6 1.0
CA A:THR69 4.9 37.8 1.0

Cadmium binding site 10 out of 17 in 7d30

Go back to Cadmium Binding Sites List in 7d30
Cadmium binding site 10 out of 17 in the Structure of Sybody MR17-SR31 Fusion in Complex with the Sars-Cov-2 S Receptor Binding Domain (Rbd)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Structure of Sybody MR17-SR31 Fusion in Complex with the Sars-Cov-2 S Receptor Binding Domain (Rbd) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1323

b:123.5
occ:0.27
CD A:CD1324 2.2 39.8 0.7
O A:VAL98 2.3 42.8 1.0
OD1 A:ASP100 2.3 35.1 1.0
OD1 A:ASP109 2.3 71.7 1.0
CG A:ASP109 3.0 64.7 1.0
O A:HOH1406 3.2 49.7 1.0
CD A:CD1317 3.3 150.8 0.6
OD2 A:ASP109 3.4 53.3 1.0
C A:VAL98 3.5 37.3 1.0
CG A:ASP100 3.5 47.0 1.0
CG1 A:VAL98 3.7 36.3 1.0
N A:ASP100 3.8 38.6 1.0
CD A:CD1325 4.0 65.1 0.3
OD1 A:ASN97 4.1 51.6 1.0
CB A:ASP109 4.1 60.3 1.0
OD2 A:ASP100 4.2 37.6 1.0
O A:HOH1468 4.3 34.5 1.0
CA A:VAL98 4.3 39.0 1.0
N A:LYS99 4.4 32.4 1.0
N A:VAL98 4.4 40.0 1.0
CA A:LYS99 4.5 36.6 1.0
CB A:ASP100 4.5 33.1 1.0
CB A:VAL98 4.6 42.8 1.0
O A:HOH1471 4.6 54.5 1.0
C A:LYS99 4.7 37.9 1.0
CA A:ASP100 4.7 38.4 1.0
CG A:ASN97 4.7 49.4 1.0
ND2 A:ASN97 4.8 41.2 1.0

Reference:

T.Li, H.Cai, H.Yao, B.Zhou, Y.Zhao, W.Qin, D.Lavillette, D.Li. Potent Synthetic Nanobodies Against Sars-Cov-2 and Molecular Basis For Neutratlization To Be Published.
Page generated: Sat Apr 17 14:38:38 2021

Last articles

Zn in 7RE3
Zn in 7RDX
Zn in 7RDZ
Zn in 7RWM
Zn in 7PGU
Zn in 7PGR
Zn in 7PGT
Zn in 7PGS
Zn in 7SQE
Zn in 7RWK
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy