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

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

Go back to Cadmium Binding Sites List in 4fkc
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

Go back to Cadmium Binding Sites List in 4fkc
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

Go back to Cadmium Binding Sites List in 4fkc
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

Go back to Cadmium Binding Sites List in 4fkc
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

Go back to Cadmium Binding Sites List in 4fkc
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

Go back to Cadmium Binding Sites List in 4fkc
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

Go back to Cadmium Binding Sites List in 4fkc
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

Go back to Cadmium Binding Sites List in 4fkc
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

Go back to Cadmium Binding Sites List in 4fkc
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

Go back to Cadmium Binding Sites List in 4fkc
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

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy