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Cadmium in PDB 4h3u: Crystal Structure of Hypothetical Protein with Ketosteroid Isomerase- Like Protein Fold From Catenulispora Acidiphila Dsm 44928

Protein crystallography data

The structure of Crystal Structure of Hypothetical Protein with Ketosteroid Isomerase- Like Protein Fold From Catenulispora Acidiphila Dsm 44928, PDB code: 4h3u was solved by E.V.Filippova, G.Minasov, L.Shuvalova, O.Kiryukhina, R.Jedrzejczak, A.Joachimiak, W.F.Anderson, Midwest Center For Structural Genomics(Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.94 / 1.15
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 61.578, 61.578, 144.576, 90.00, 90.00, 120.00
R / Rfree (%) 12.8 / 14.3

Other elements in 4h3u:

The structure of Crystal Structure of Hypothetical Protein with Ketosteroid Isomerase- Like Protein Fold From Catenulispora Acidiphila Dsm 44928 also contains other interesting chemical elements:

Chlorine (Cl) 9 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of Hypothetical Protein with Ketosteroid Isomerase- Like Protein Fold From Catenulispora Acidiphila Dsm 44928 (pdb code 4h3u). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 7 binding sites of Cadmium where determined in the Crystal Structure of Hypothetical Protein with Ketosteroid Isomerase- Like Protein Fold From Catenulispora Acidiphila Dsm 44928, PDB code: 4h3u:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7;

Cadmium binding site 1 out of 7 in 4h3u

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Cadmium binding site 1 out of 7 in the Crystal Structure of Hypothetical Protein with Ketosteroid Isomerase- Like Protein Fold From Catenulispora Acidiphila Dsm 44928


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 Hypothetical Protein with Ketosteroid Isomerase- Like Protein Fold From Catenulispora Acidiphila Dsm 44928 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd201

b:13.5
occ:1.00
OE1 A:GLU45 2.3 12.4 1.0
O A:HOH333 2.4 46.3 1.0
CD A:GLU45 3.0 9.9 1.0
OE2 A:GLU45 3.0 17.2 1.0
O A:HOH371 4.3 19.4 1.0
CG A:GLU45 4.4 7.9 1.0

Cadmium binding site 2 out of 7 in 4h3u

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Cadmium binding site 2 out of 7 in the Crystal Structure of Hypothetical Protein with Ketosteroid Isomerase- Like Protein Fold From Catenulispora Acidiphila Dsm 44928


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 Hypothetical Protein with Ketosteroid Isomerase- Like Protein Fold From Catenulispora Acidiphila Dsm 44928 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd202

b:9.3
occ:0.90
CL B:CL204 2.4 11.0 1.0
CL A:CL205 2.4 11.1 1.0
O B:TYR114 2.4 7.4 1.0
O A:TYR114 2.4 7.3 1.0
CL A:CL206 2.5 12.1 1.0
C A:TYR114 3.3 7.1 1.0
C B:TYR114 3.3 7.3 1.0
N A:TYR114 3.9 7.9 1.0
N B:TYR114 3.9 7.7 1.0
N B:SER115 4.0 8.0 1.0
N A:SER115 4.0 7.6 1.0
CA B:SER115 4.0 8.4 1.0
CA A:SER115 4.0 7.8 1.0
CA A:TYR114 4.2 7.6 1.0
CA B:TYR114 4.2 7.8 1.0
N A:LEU116 4.6 8.1 1.0
N B:LEU116 4.6 8.2 1.0
CB A:ALA36 4.7 10.6 1.0
CB B:ALA36 4.7 10.9 1.0
O B:HOH325 4.8 16.0 1.0
O A:HOH328 4.8 16.8 1.0
CA A:ALA36 4.8 9.9 1.0
CA B:ALA36 4.8 10.2 1.0
C B:SER115 4.8 8.2 1.0
C A:SER115 4.8 7.8 1.0
C A:TYR113 4.9 7.7 1.0
C B:TYR113 4.9 8.0 1.0

Cadmium binding site 3 out of 7 in 4h3u

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Cadmium binding site 3 out of 7 in the Crystal Structure of Hypothetical Protein with Ketosteroid Isomerase- Like Protein Fold From Catenulispora Acidiphila Dsm 44928


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 Hypothetical Protein with Ketosteroid Isomerase- Like Protein Fold From Catenulispora Acidiphila Dsm 44928 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd203

b:22.4
occ:1.00
O A:HOH414 2.2 33.2 1.0
NE2 A:HIS62 2.3 15.3 1.0
OXT A:ACT212 2.3 38.2 1.0
O A:HOH435 2.3 30.3 1.0
O A:HOH401 2.3 25.6 1.0
O A:ACT212 2.4 26.1 1.0
C A:ACT212 2.7 28.4 1.0
CD2 A:HIS62 3.2 14.7 1.0
CE1 A:HIS62 3.3 13.8 1.0
CH3 A:ACT212 4.2 35.7 1.0
O A:HOH363 4.2 21.0 1.0
O A:HOH436 4.3 39.4 1.0
O A:HOH458 4.3 24.0 1.0
CG A:HIS62 4.4 12.9 1.0
ND1 A:HIS62 4.4 12.6 1.0
O A:HOH472 4.4 31.0 1.0
O A:HOH329 4.6 17.4 1.0
O A:HOH505 4.7 40.7 1.0
CB A:ALA93 4.9 9.7 1.0

Cadmium binding site 4 out of 7 in 4h3u

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Cadmium binding site 4 out of 7 in the Crystal Structure of Hypothetical Protein with Ketosteroid Isomerase- Like Protein Fold From Catenulispora Acidiphila Dsm 44928


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 Hypothetical Protein with Ketosteroid Isomerase- Like Protein Fold From Catenulispora Acidiphila Dsm 44928 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd204

b:37.6
occ:1.00
O A:ACT210 2.2 43.2 1.0
NE2 A:HIS74 2.2 23.1 1.0
O A:HOH471 2.3 31.6 1.0
O A:ACT211 2.4 51.1 1.0
OXT A:ACT211 2.6 61.5 1.0
CL A:CL209 2.7 33.0 0.5
OXT A:ACT210 2.7 38.0 1.0
C A:ACT210 2.8 38.3 1.0
C A:ACT211 2.8 53.1 1.0
CL B:CL205 3.1 43.5 1.0
CD2 A:HIS74 3.1 20.3 1.0
CE1 A:HIS74 3.3 21.3 1.0
CL A:CL209 3.3 21.3 0.5
CG A:HIS74 4.3 15.1 1.0
CH3 A:ACT210 4.3 36.2 1.0
ND1 A:HIS74 4.3 17.5 1.0
CH3 A:ACT211 4.4 54.1 1.0
O A:HOH484 4.7 44.9 1.0

Cadmium binding site 5 out of 7 in 4h3u

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Cadmium binding site 5 out of 7 in the Crystal Structure of Hypothetical Protein with Ketosteroid Isomerase- Like Protein Fold From Catenulispora Acidiphila Dsm 44928


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 Hypothetical Protein with Ketosteroid Isomerase- Like Protein Fold From Catenulispora Acidiphila Dsm 44928 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd201

b:18.4
occ:0.70
O B:HOH453 2.2 29.3 1.0
O B:ACT206 2.2 29.4 0.5
O B:HOH377 2.2 25.4 1.0
NE2 B:HIS62 2.3 13.9 1.0
O B:HOH454 2.3 33.9 1.0
OXT B:ACT206 2.4 39.7 0.5
OXT B:ACT206 2.4 21.3 0.5
C B:ACT206 2.6 26.1 0.5
O B:ACT206 2.7 50.9 0.5
C B:ACT206 2.9 33.0 0.5
CD2 B:HIS62 3.2 15.4 1.0
CE1 B:HIS62 3.3 13.4 1.0
CH3 B:ACT206 4.1 29.4 0.5
O B:HOH359 4.2 20.6 1.0
O B:HOH468 4.3 25.1 1.0
O B:HOH476 4.4 37.1 1.0
CG B:HIS62 4.4 13.1 1.0
ND1 B:HIS62 4.4 12.8 1.0
O B:HOH392 4.4 33.2 1.0
O B:HOH475 4.4 40.1 1.0
CH3 B:ACT206 4.4 24.5 0.5
O B:HOH329 4.6 17.6 1.0
O B:HOH455 4.8 42.2 1.0
CB B:ALA93 4.9 10.0 1.0

Cadmium binding site 6 out of 7 in 4h3u

Go back to Cadmium Binding Sites List in 4h3u
Cadmium binding site 6 out of 7 in the Crystal Structure of Hypothetical Protein with Ketosteroid Isomerase- Like Protein Fold From Catenulispora Acidiphila Dsm 44928


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 Hypothetical Protein with Ketosteroid Isomerase- Like Protein Fold From Catenulispora Acidiphila Dsm 44928 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd202

b:13.5
occ:1.00
ND1 B:HIS84 2.2 7.7 1.0
CE1 B:HIS84 3.1 7.2 1.0
CG B:HIS84 3.3 7.3 1.0
CB B:HIS84 3.7 6.8 1.0
NE2 B:HIS84 4.3 7.4 1.0
CD2 B:HIS84 4.4 7.9 1.0
ND2 B:ASN60 4.5 23.7 0.5
CB B:PRO91 4.6 7.5 1.0
CD B:PRO91 4.7 7.0 1.0
CG B:PRO91 4.7 8.1 1.0
O B:HOH336 5.0 18.9 1.0

Cadmium binding site 7 out of 7 in 4h3u

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Cadmium binding site 7 out of 7 in the Crystal Structure of Hypothetical Protein with Ketosteroid Isomerase- Like Protein Fold From Catenulispora Acidiphila Dsm 44928


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 Hypothetical Protein with Ketosteroid Isomerase- Like Protein Fold From Catenulispora Acidiphila Dsm 44928 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd203

b:36.6
occ:1.00
O B:HOH430 2.3 34.8 1.0
NE2 B:HIS74 2.3 23.5 1.0
O B:HOH480 2.4 23.8 1.0
O A:HOH426 2.4 37.0 0.5
O A:HOH426 2.7 25.5 0.5
CL A:CL207 2.7 33.4 0.5
CL A:CL208 3.0 44.8 1.0
CL A:CL207 3.3 21.1 0.5
CD2 B:HIS74 3.3 20.6 1.0
CE1 B:HIS74 3.3 24.7 1.0
O B:HOH481 3.7 36.3 1.0
ND1 B:HIS74 4.4 18.8 1.0
CG B:HIS74 4.4 15.9 1.0

Reference:

E.V.Filippova, C.H.Luan, S.F.Dunne, O.Kiryukhina, G.Minasov, L.Shuvalova, W.F.Anderson. Structural Characterization of A Hypothetical Protein: A Potential Agent Involved in Trimethylamine Metabolism in Catenulispora Acidiphila. J.Struct.Funct.Genom. V. 15 33 2014.
ISSN: ISSN 1345-711X
PubMed: 24562475
DOI: 10.1007/S10969-014-9176-Z
Page generated: Sat Dec 12 08:24:43 2020

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