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Zinc in PDB 4rgz: Crystal Structure of Recombinant Prolidase From Thermococcus Sibiricus at P21221 Spacegroup

Protein crystallography data

The structure of Crystal Structure of Recombinant Prolidase From Thermococcus Sibiricus at P21221 Spacegroup, PDB code: 4rgz was solved by V.I.Timofeev, D.A.Korgenevsky, M.A.Gorbacheva, K.M.Boyko, E.Slutsky, T.V.Rakitina, A.V.Lipkin, V.O.Popov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.48 / 2.60
Space group P 21 2 21
Cell size a, b, c (Å), α, β, γ (°) 97.600, 123.720, 136.520, 90.00, 90.00, 90.00
R / Rfree (%) 22.1 / 29.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Recombinant Prolidase From Thermococcus Sibiricus at P21221 Spacegroup (pdb code 4rgz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Recombinant Prolidase From Thermococcus Sibiricus at P21221 Spacegroup, PDB code: 4rgz:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 4rgz

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Zinc binding site 1 out of 8 in the Crystal Structure of Recombinant Prolidase From Thermococcus Sibiricus at P21221 Spacegroup


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Recombinant Prolidase From Thermococcus Sibiricus at P21221 Spacegroup within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:50.0
occ:1.00
 OD1 A:ASP240 2.1 30.6 1.0
O A:HOH518 2.1 32.5 1.0
OD1 A:ASP229 2.1 26.7 1.0
OE1 A:GLU347 2.2 32.3 1.0
OE2 A:GLU347 2.7 31.9 1.0
CD A:GLU347 2.8 31.9 1.0
CG A:ASP240 2.8 29.7 1.0
CG A:ASP229 2.8 26.2 1.0
OD2 A:ASP229 2.9 26.1 1.0
OD2 A:ASP240 3.0 29.7 1.0
OG1 A:THR242 3.4 26.9 1.0
OE1 A:GLU333 3.5 32.1 1.0
CZ A:PHE198 4.1 22.8 1.0
CB A:ASP240 4.2 27.4 1.0
O A:VAL241 4.2 26.8 1.0
CG A:GLU347 4.3 29.8 1.0
CB A:ASP229 4.3 25.4 1.0
CD A:GLU333 4.4 32.8 1.0
O A:HOH543 4.5 61.3 1.0
C A:ASP240 4.5 26.9 1.0
C A:VAL241 4.5 25.9 1.0
N A:VAL241 4.5 25.5 1.0
CA A:ASP240 4.7 26.4 1.0
OE2 A:GLU333 4.7 37.1 1.0
CE2 A:PHE198 4.8 23.6 1.0
CB A:THR242 4.8 27.7 1.0
NE2 A:HIS304 4.8 38.3 1.0
O A:ASP240 4.8 26.4 1.0
CB A:GLU347 4.8 29.9 1.0
N A:THR242 4.9 26.0 1.0
CA A:ASP229 4.9 24.9 1.0
CE1 A:PHE198 4.9 22.4 1.0
O A:TYR230 5.0 28.0 1.0
N A:TYR230 5.0 24.8 1.0
CA A:VAL241 5.0 24.6 1.0

Zinc binding site 2 out of 8 in 4rgz

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Zinc binding site 2 out of 8 in the Crystal Structure of Recombinant Prolidase From Thermococcus Sibiricus at P21221 Spacegroup


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Recombinant Prolidase From Thermococcus Sibiricus at P21221 Spacegroup within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:93.2
occ:1.00
 NE A:ARG301 3.5 32.9 1.0
NH2 A:ARG301 3.6 36.2 1.0
CD2 A:HIS304 3.6 35.9 1.0
OE2 A:GLU333 3.9 37.1 1.0
NH1 N:ARG49 3.9 95.1 1.0
CZ A:ARG301 4.0 35.5 1.0
NE2 A:HIS311 4.0 31.9 1.0
NE2 A:HIS304 4.2 38.3 1.0
O A:HOH503 4.2 30.9 1.0
CE1 A:HIS311 4.5 32.3 1.0
CG A:ARG301 4.5 27.6 1.0
CG A:HIS304 4.6 35.5 1.0
NH2 N:ARG49 4.6 0.2 1.0
CD A:ARG301 4.6 30.7 1.0
CZ N:ARG49 4.8 98.4 1.0
CD2 A:HIS311 4.8 34.2 1.0
CD A:GLU333 4.9 32.8 1.0
O A:HOH518 4.9 32.5 1.0
O A:HOH504 4.9 50.4 1.0

Zinc binding site 3 out of 8 in 4rgz

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Zinc binding site 3 out of 8 in the Crystal Structure of Recombinant Prolidase From Thermococcus Sibiricus at P21221 Spacegroup


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Recombinant Prolidase From Thermococcus Sibiricus at P21221 Spacegroup within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn401

b:77.6
occ:1.00
 O N:HOH548 2.3 35.9 1.0
ZN N:ZN402 3.3 91.2 1.0
OD2 N:ASP229 3.7 39.6 1.0
OE1 N:GLU333 4.0 36.9 1.0
NE2 N:HIS304 4.0 32.3 1.0
OD2 N:ASP240 4.0 32.4 1.0
OE2 N:GLU333 4.1 37.8 1.0
NE2 N:HIS311 4.1 35.7 1.0
O N:HOH533 4.3 45.9 1.0
OE1 N:GLU347 4.3 36.4 1.0
CD N:GLU333 4.5 37.1 1.0
OE2 N:GLU347 4.5 36.0 1.0
CG N:ASP229 4.5 37.0 1.0
OD1 N:ASP229 4.6 41.4 1.0
CD2 N:HIS304 4.6 33.8 1.0
OD1 N:ASP240 4.6 31.2 1.0
CG N:ASP240 4.8 31.6 1.0
CE1 N:HIS311 4.9 36.5 1.0
CD N:GLU347 4.9 33.2 1.0

Zinc binding site 4 out of 8 in 4rgz

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Zinc binding site 4 out of 8 in the Crystal Structure of Recombinant Prolidase From Thermococcus Sibiricus at P21221 Spacegroup


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Recombinant Prolidase From Thermococcus Sibiricus at P21221 Spacegroup within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn402

b:91.2
occ:1.00
 OD1 N:ASP240 2.0 31.2 1.0
OD1 N:ASP229 2.0 41.4 1.0
OE1 N:GLU347 2.3 36.4 1.0
CG N:ASP240 2.8 31.6 1.0
O N:HOH548 2.8 35.9 1.0
CG N:ASP229 2.9 37.0 1.0
CD N:GLU347 3.0 33.2 1.0
OD2 N:ASP240 3.0 32.4 1.0
OD2 N:ASP229 3.0 39.6 1.0
OE2 N:GLU347 3.1 36.0 1.0
ZN N:ZN401 3.3 77.6 1.0
OG1 N:THR242 3.5 24.2 1.0
CZ N:PHE198 4.0 24.5 1.0
CB N:ASP240 4.1 31.3 1.0
N N:VAL241 4.2 26.7 1.0
O N:VAL241 4.2 27.7 1.0
C N:ASP240 4.3 28.0 1.0
CB N:ASP229 4.3 35.3 1.0
CG N:GLU347 4.3 31.3 1.0
CE1 N:PHE198 4.4 25.1 1.0
C N:VAL241 4.4 26.6 1.0
CA N:ASP240 4.4 30.2 1.0
OE1 N:GLU333 4.5 36.9 1.0
O N:ASP240 4.7 30.6 1.0
CA N:ASP229 4.8 33.4 1.0
CA N:VAL241 4.8 27.3 1.0
N N:TYR230 4.8 29.9 1.0
CB N:THR242 4.9 26.1 1.0
N N:THR242 4.9 27.1 1.0
CE2 N:PHE198 4.9 26.4 1.0
C N:ASP229 5.0 33.7 1.0
CB N:GLU347 5.0 30.8 1.0
OE2 N:GLU333 5.0 37.8 1.0

Zinc binding site 5 out of 8 in 4rgz

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Zinc binding site 5 out of 8 in the Crystal Structure of Recombinant Prolidase From Thermococcus Sibiricus at P21221 Spacegroup


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Recombinant Prolidase From Thermococcus Sibiricus at P21221 Spacegroup within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Zn401

b:58.8
occ:1.00
 OD1 1:ASP229 2.0 41.2 1.0
OD1 1:ASP240 2.2 34.6 1.0
OE1 1:GLU347 2.2 39.0 1.0
CG 1:ASP240 2.8 33.6 1.0
OE2 1:GLU347 2.8 38.1 1.0
CG 1:ASP229 2.8 39.2 1.0
CD 1:GLU347 2.9 38.5 1.0
OD2 1:ASP240 2.9 30.6 1.0
OD2 1:ASP229 3.0 37.2 1.0
OG1 1:THR242 3.4 35.8 1.0
ZN 1:ZN404 3.4 0.7 1.0
OE1 1:GLU333 4.0 42.5 1.0
CB 1:ASP240 4.1 34.3 1.0
CZ 1:PHE198 4.1 40.5 1.0
O 1:HOH511 4.2 58.1 1.0
N 1:VAL241 4.2 36.5 1.0
O 1:VAL241 4.3 39.4 1.0
CB 1:ASP229 4.3 37.7 1.0
CG 1:GLU347 4.3 38.5 1.0
C 1:ASP240 4.4 36.1 1.0
C 1:VAL241 4.5 38.0 1.0
CA 1:ASP240 4.6 35.8 1.0
CE1 1:PHE198 4.7 39.8 1.0
NE2 1:HIS304 4.7 35.6 1.0
CD 1:GLU333 4.8 39.8 1.0
CA 1:ASP229 4.8 39.0 1.0
CE2 1:PHE198 4.8 40.4 1.0
CB 1:THR242 4.8 34.9 1.0
OE2 1:GLU333 4.8 39.8 1.0
N 1:THR242 4.9 38.0 1.0
CA 1:VAL241 4.9 37.8 1.0
CB 1:GLU347 4.9 38.3 1.0
N 1:TYR230 4.9 38.2 1.0
O 1:TYR230 5.0 45.5 1.0

Zinc binding site 6 out of 8 in 4rgz

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Zinc binding site 6 out of 8 in the Crystal Structure of Recombinant Prolidase From Thermococcus Sibiricus at P21221 Spacegroup


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Recombinant Prolidase From Thermococcus Sibiricus at P21221 Spacegroup within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Zn404

b:0.7
occ:1.00
 O4 1:PO4402 2.4 49.9 1.0
O 1:HOH511 3.1 58.1 1.0
OE1 1:GLU333 3.3 42.5 1.0
ZN 1:ZN401 3.4 58.8 1.0
OD2 1:ASP229 3.4 37.2 1.0
O 1:HOH515 3.5 48.0 1.0
O1 1:PO4402 3.6 49.0 1.0
P 1:PO4402 3.6 52.4 1.0
OE2 1:GLU333 3.9 39.8 1.0
NE2 1:HIS304 3.9 35.6 1.0
CD 1:GLU333 4.0 39.8 1.0
OD2 1:ASP240 4.3 30.6 1.0
CE1 1:HIS212 4.3 40.3 1.0
OE2 1:GLU347 4.3 38.1 1.0
CD2 1:HIS304 4.4 35.6 1.0
CG 1:ASP229 4.4 39.2 1.0
CE1 1:HIS311 4.5 37.2 1.0
O3 1:PO4402 4.5 50.0 1.0
OD1 1:ASP229 4.6 41.2 1.0
O2 1:PO4402 4.7 54.6 1.0
NE2 1:HIS311 4.9 37.1 1.0
NH1 1:ARG345 4.9 45.1 1.0

Zinc binding site 7 out of 8 in 4rgz

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Zinc binding site 7 out of 8 in the Crystal Structure of Recombinant Prolidase From Thermococcus Sibiricus at P21221 Spacegroup


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Recombinant Prolidase From Thermococcus Sibiricus at P21221 Spacegroup within 5.0Å range:
probe atom residue distance (Å) B Occ
e:Zn401

b:70.8
occ:1.00
 OD1 e:ASP240 2.1 46.6 1.0
OE1 e:GLU347 2.2 36.7 1.0
OD1 e:ASP229 2.3 41.6 1.0
ZN e:ZN402 2.8 0.1 1.0
OE2 e:GLU347 2.8 39.2 1.0
CD e:GLU347 2.8 38.0 1.0
CG e:ASP240 2.9 42.1 1.0
OD2 e:ASP229 2.9 42.1 1.0
CG e:ASP229 2.9 39.1 1.0
OD2 e:ASP240 2.9 42.2 1.0
OG1 e:THR242 3.4 36.0 1.0
CZ e:PHE198 4.0 38.2 1.0
OE1 e:GLU333 4.1 47.2 1.0
CG e:GLU347 4.3 36.8 1.0
CB e:ASP240 4.3 39.6 1.0
O e:VAL241 4.3 30.5 1.0
CB e:ASP229 4.4 36.0 1.0
C e:ASP240 4.4 36.0 1.0
N e:VAL241 4.5 33.1 1.0
C e:VAL241 4.5 31.3 1.0
O e:ASP240 4.6 37.7 1.0
NH1 e:ARG345 4.6 40.8 1.0
CE1 e:PHE198 4.6 38.0 1.0
CB e:THR242 4.8 34.8 1.0
CD e:GLU333 4.8 46.5 1.0
CA e:ASP240 4.8 36.8 1.0
NE2 e:HIS304 4.8 43.9 1.0
CE2 e:PHE198 4.8 37.5 1.0
N e:THR242 4.8 32.1 1.0
CB e:GLU347 4.9 37.1 1.0
CA e:ASP229 4.9 34.8 1.0
N e:TYR230 4.9 32.4 1.0
CA e:VAL241 4.9 31.4 1.0
C e:ASP229 5.0 33.8 1.0

Zinc binding site 8 out of 8 in 4rgz

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Zinc binding site 8 out of 8 in the Crystal Structure of Recombinant Prolidase From Thermococcus Sibiricus at P21221 Spacegroup


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Recombinant Prolidase From Thermococcus Sibiricus at P21221 Spacegroup within 5.0Å range:
probe atom residue distance (Å) B Occ
e:Zn402

b:0.1
occ:1.00
 ZN e:ZN401 2.8 70.8 1.0
NE2 e:HIS304 3.0 43.9 1.0
OE1 e:GLU333 3.1 47.2 1.0
OE2 e:GLU333 3.2 49.7 1.0
OE2 e:GLU347 3.3 39.2 1.0
CD e:GLU333 3.5 46.5 1.0
OD2 e:ASP240 3.5 42.2 1.0
CE1 e:HIS304 3.9 42.8 1.0
CD2 e:HIS304 4.0 44.2 1.0
OD2 e:ASP229 4.0 42.1 1.0
O e:HOH508 4.1 52.5 1.0
CD e:GLU347 4.1 38.0 1.0
OE1 e:GLU347 4.2 36.7 1.0
OD1 e:ASP240 4.3 46.6 1.0
CG e:ASP240 4.3 42.1 1.0
OD1 e:ASP229 4.6 41.6 1.0
CE1 e:HIS311 4.7 49.7 1.0
CG e:ASP229 4.7 39.1 1.0
CG e:GLU333 4.9 44.1 1.0

Reference:

V.Timofeev, E.Slutskaya, M.Gorbacheva, K.Boyko, T.Rakitina, D.Korzhenevskiy, A.Lipkin, V.Popov. Structure of Recombinant Prolidase From Thermococcus Sibiricus in Space Group P21221. Acta Crystallogr.,Sect.F V. 71 951 2015.
PubMed: 26249680
DOI: 10.1107/S2053230X15009498
Page generated: Sun Oct 27 07:07:51 2024

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