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Cadmium in PDB 4fkc: Recombinant Prolidase From Thermococcus Sibiricus

Protein crystallography data

The structure of Recombinant Prolidase From Thermococcus Sibiricus, PDB code: 4fkc was solved by A.A.Trofimov, E.S.Slutskaya, K.M.Polyakov, P.V.Dorovatovskii, V.M.Gumerov, V.O.Popov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 78.83 / 2.60
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 89.700, 89.700, 165.220, 90.00, 90.00, 90.00
R / Rfree (%) 23.1 / 26.9

Cadmium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Cadmium atom in the Recombinant Prolidase From Thermococcus Sibiricus (pdb code 4fkc). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 12 binding sites of Cadmium where determined in the Recombinant Prolidase From Thermococcus Sibiricus, PDB code: 4fkc:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 12 in 4fkc

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Cadmium binding site 1 out of 12 in the Recombinant Prolidase From Thermococcus Sibiricus


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Recombinant Prolidase From Thermococcus Sibiricus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd401

b:47.9
occ:1.00
OE2 A:GLU347 2.2 44.0 1.0
OE2 A:GLU333 2.2 47.8 1.0
OD2 A:ASP240 2.2 42.3 1.0
NE2 A:HIS304 2.3 44.8 1.0
OE1 A:GLU333 2.8 48.0 1.0
CD A:GLU333 2.9 48.5 1.0
O A:HOH551 2.9 49.5 1.0
O A:HOH549 2.9 39.0 1.0
CD A:CD402 3.1 46.2 1.0
CD A:GLU347 3.1 41.4 1.0
CG A:ASP240 3.3 39.5 1.0
CE1 A:HIS304 3.3 44.3 1.0
CD2 A:HIS304 3.3 45.1 1.0
OE1 A:GLU347 3.4 44.0 1.0
OD1 A:ASP240 3.8 43.8 1.0
CG2 A:THR331 4.3 40.2 1.0
OG1 A:THR331 4.3 40.3 1.0
CG A:GLU333 4.4 45.0 1.0
ND1 A:HIS304 4.4 44.0 1.0
CB A:ASP240 4.4 38.9 1.0
CG A:HIS304 4.4 43.5 1.0
CG A:GLU347 4.5 39.9 1.0
CB A:THR331 4.6 40.8 1.0
NE2 A:HIS311 4.8 53.4 1.0
OD2 A:ASP229 5.0 40.3 1.0

Cadmium binding site 2 out of 12 in 4fkc

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Cadmium binding site 2 out of 12 in the Recombinant Prolidase From Thermococcus Sibiricus


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Recombinant Prolidase From Thermococcus Sibiricus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd402

b:46.2
occ:1.00
OD1 A:ASP240 2.2 43.8 1.0
OE1 A:GLU347 2.2 44.0 1.0
OD2 A:ASP229 2.2 40.3 1.0
OD1 A:ASP229 2.2 39.3 1.0
CG A:ASP229 2.5 39.9 1.0
O A:HOH549 2.8 39.0 1.0
OD2 A:ASP240 2.9 42.3 1.0
CG A:ASP240 2.9 39.5 1.0
CD A:GLU347 3.1 41.4 1.0
CD A:CD401 3.1 47.9 1.0
OE2 A:GLU347 3.3 44.0 1.0
OG1 A:THR242 3.5 38.1 1.0
OE1 A:GLU333 3.7 48.0 1.0
CB A:ASP229 4.0 40.0 1.0
CZ A:PHE198 4.2 45.6 1.0
CB A:ASP240 4.3 38.9 1.0
CG A:GLU347 4.5 39.9 1.0
CD A:GLU333 4.6 48.5 1.0
NH1 A:ARG345 4.6 46.3 1.0
OE2 A:GLU333 4.8 47.8 1.0
O A:HOH551 4.8 49.5 1.0
CE1 A:PHE198 4.8 45.0 1.0
C A:ASP240 4.8 38.5 1.0
CA A:ASP229 4.9 40.1 1.0
CE2 A:PHE198 4.9 46.1 1.0
CB A:THR242 4.9 39.2 1.0
CA A:ASP240 4.9 38.4 1.0
O A:VAL241 5.0 38.0 1.0
N A:VAL241 5.0 38.2 1.0
CB A:GLU347 5.0 39.5 1.0

Cadmium binding site 3 out of 12 in 4fkc

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Cadmium binding site 3 out of 12 in the Recombinant Prolidase From Thermococcus Sibiricus


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Recombinant Prolidase From Thermococcus Sibiricus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd403

b:42.6
occ:1.00
OE1 A:GLU366 2.2 43.3 1.0
O A:HOH527 2.4 13.1 1.0
O A:HOH528 2.5 3.9 1.0
O A:HOH529 2.6 23.0 1.0
CD A:GLU366 3.0 43.6 1.0
OE2 A:GLU366 3.0 46.6 1.0
CG A:GLU366 4.4 42.6 1.0

Cadmium binding site 4 out of 12 in 4fkc

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Cadmium binding site 4 out of 12 in the Recombinant Prolidase From Thermococcus Sibiricus


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Recombinant Prolidase From Thermococcus Sibiricus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd404

b:43.0
occ:1.00
OE1 A:GLU99 2.2 41.8 1.0
OE2 A:GLU99 2.2 34.1 1.0
O A:HOH531 2.4 15.6 1.0
CD A:GLU99 2.5 37.1 1.0
O A:HOH530 2.7 26.4 1.0
CG A:GLU99 4.1 44.5 1.0
CE A:LYS96 4.5 58.4 1.0
NZ A:LYS96 4.7 60.1 1.0
CB A:GLU99 4.9 48.5 1.0

Cadmium binding site 5 out of 12 in 4fkc

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Cadmium binding site 5 out of 12 in the Recombinant Prolidase From Thermococcus Sibiricus


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Recombinant Prolidase From Thermococcus Sibiricus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd405

b:66.3
occ:0.50
O A:LEU370 2.2 61.5 1.0
O A:HOH544 2.3 13.1 0.5
O A:HOH545 2.4 17.5 0.5
OXT A:LEU370 2.6 59.7 1.0
C A:LEU370 2.8 59.0 1.0
CD A:CD406 3.6 85.2 0.5
N A:GLY248 4.0 56.9 1.0
CA A:GLY248 4.3 58.1 1.0
CA A:LEU370 4.3 57.4 1.0
OE2 A:GLU172 4.6 76.3 1.0
CG1 A:VAL247 5.0 54.8 1.0

Cadmium binding site 6 out of 12 in 4fkc

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Cadmium binding site 6 out of 12 in the Recombinant Prolidase From Thermococcus Sibiricus


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Recombinant Prolidase From Thermococcus Sibiricus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd406

b:85.2
occ:0.50
OE2 A:GLU172 2.2 76.3 1.0
CD A:GLU172 3.2 73.5 1.0
CD A:CD405 3.6 66.3 0.5
OE1 A:GLU172 3.6 74.8 1.0
O A:HOH544 3.7 13.1 0.5
CG A:GLU172 4.5 69.0 1.0
CB A:LYS222 4.6 59.0 1.0
O A:HOH545 4.9 17.5 0.5

Cadmium binding site 7 out of 12 in 4fkc

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Cadmium binding site 7 out of 12 in the Recombinant Prolidase From Thermococcus Sibiricus


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Recombinant Prolidase From Thermococcus Sibiricus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd407

b:75.3
occ:0.50
OD2 A:ASP195 2.2 65.9 1.0
CG A:ASP195 3.4 59.0 1.0
OD1 A:ASP195 4.3 58.4 1.0
CB A:ASP195 4.3 56.0 1.0
O A:HOH550 4.6 37.3 1.0
O A:ASP194 4.8 58.4 1.0

Cadmium binding site 8 out of 12 in 4fkc

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Cadmium binding site 8 out of 12 in the Recombinant Prolidase From Thermococcus Sibiricus


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Recombinant Prolidase From Thermococcus Sibiricus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd408

b:55.9
occ:1.00
O A:HOH540 1.9 27.9 1.0
O A:HOH541 2.1 18.6 1.0
OD1 A:ASP147 2.2 49.6 1.0
NE2 A:HIS2 2.3 55.6 1.0
OD2 A:ASP147 2.7 48.8 1.0
CG A:ASP147 2.8 45.9 1.0
CE1 A:HIS2 3.1 54.4 1.0
CD2 A:HIS2 3.5 53.8 1.0
CB A:ASP147 4.2 43.2 1.0
ND1 A:HIS2 4.3 55.1 1.0
O A:HOH552 4.5 53.5 1.0
CG A:HIS2 4.5 55.2 1.0

Cadmium binding site 9 out of 12 in 4fkc

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Cadmium binding site 9 out of 12 in the Recombinant Prolidase From Thermococcus Sibiricus


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Recombinant Prolidase From Thermococcus Sibiricus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd409

b:54.4
occ:1.00
ND1 A:HIS3 2.3 48.4 1.0
O A:HOH538 2.4 23.7 1.0
CG A:HIS3 3.2 49.1 1.0
CE1 A:HIS3 3.4 48.6 1.0
CB A:HIS3 3.4 49.7 1.0
CA A:HIS3 3.9 50.0 1.0
CD2 A:HIS3 4.4 46.6 1.0
NE2 A:HIS3 4.4 49.6 1.0
N A:HIS3 4.7 51.8 1.0

Cadmium binding site 10 out of 12 in 4fkc

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Cadmium binding site 10 out of 12 in the Recombinant Prolidase From Thermococcus Sibiricus


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Recombinant Prolidase From Thermococcus Sibiricus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd410

b:76.6
occ:0.50
OE2 A:GLU75 2.2 67.0 1.0
CD A:GLU75 3.0 62.8 1.0
OE1 A:GLU75 3.0 65.9 1.0
O A:HOH542 3.8 40.8 1.0
CG A:GLU75 4.4 56.9 1.0

Reference:

A.A.Trofimov, E.A.Slutskaya, K.M.Polyakov, P.V.Dorovatovskii, V.M.Gumerov, V.O.Popov. Influence of Intermolecular Contacts on the Structure of Recombinant Prolidase From Thermococcus Sibiricus. Acta Crystallogr.,Sect.F V. 68 1275 2012.
ISSN: ESSN 1744-3091
PubMed: 23143231
DOI: 10.1107/S174430911203761X
Page generated: Sat Dec 12 08:24:32 2020

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