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Zinc in PDB 4dlm: Crystal Structure of An Amidohydrolase (COG3618) From Burkholderia Multivorans (Target Efi-500235) with Bound Zn, Space Group P212121

Protein crystallography data

The structure of Crystal Structure of An Amidohydrolase (COG3618) From Burkholderia Multivorans (Target Efi-500235) with Bound Zn, Space Group P212121, PDB code: 4dlm was solved by M.W.Vetting, R.Toro, R.Bhosle, R.D.Seidel, B.Hillerich, E.Washington, A.Scott Glenn, S.Chowdhury, B.Evans, J.Hammonds, N.F.Al Obaidi, W.D.Zencheck, H.J.Imker, J.A.Gerlt, F.M.Raushel, S.C.Almo, Enzymefunction Initiative (Efi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.65 / 1.93
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.860, 63.200, 76.220, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 23.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of An Amidohydrolase (COG3618) From Burkholderia Multivorans (Target Efi-500235) with Bound Zn, Space Group P212121 (pdb code 4dlm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Crystal Structure of An Amidohydrolase (COG3618) From Burkholderia Multivorans (Target Efi-500235) with Bound Zn, Space Group P212121, PDB code: 4dlm:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 4dlm

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Zinc binding site 1 out of 7 in the Crystal Structure of An Amidohydrolase (COG3618) From Burkholderia Multivorans (Target Efi-500235) with Bound Zn, Space Group P212121


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 An Amidohydrolase (COG3618) From Burkholderia Multivorans (Target Efi-500235) with Bound Zn, Space Group P212121 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:22.3
occ:1.00
OD1 A:ASP244 1.9 13.8 1.0
O A:HOH503 2.0 15.8 1.0
NE2 A:HIS11 2.1 10.2 1.0
O A:HOH538 2.1 26.9 1.0
NE2 A:HIS9 2.2 21.7 1.0
CD2 A:HIS11 3.0 10.0 1.0
CG A:ASP244 3.0 12.3 1.0
CE1 A:HIS11 3.1 13.3 1.0
CD2 A:HIS9 3.2 20.7 1.0
CE1 A:HIS9 3.2 20.7 1.0
NE2 A:HIS166 3.5 35.7 1.0
OD2 A:ASP244 3.5 15.6 1.0
O A:HOH646 3.8 45.8 1.0
CE1 A:HIS166 3.9 31.2 1.0
O A:HOH507 4.1 20.3 1.0
CG A:HIS11 4.2 10.7 1.0
ND1 A:HIS11 4.2 11.9 1.0
CB A:ASP244 4.3 12.1 1.0
ND1 A:HIS9 4.3 19.9 1.0
CG A:HIS9 4.4 20.7 1.0
NH2 A:ARG106 4.6 16.1 1.0
CA A:ASP244 4.6 16.1 1.0
CG2 A:VAL247 4.7 15.2 1.0
NH1 A:ARG106 4.8 20.4 1.0
CD2 A:HIS166 4.8 33.3 1.0
O A:ASP244 5.0 16.8 1.0

Zinc binding site 2 out of 7 in 4dlm

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Zinc binding site 2 out of 7 in the Crystal Structure of An Amidohydrolase (COG3618) From Burkholderia Multivorans (Target Efi-500235) with Bound Zn, Space Group P212121


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 An Amidohydrolase (COG3618) From Burkholderia Multivorans (Target Efi-500235) with Bound Zn, Space Group P212121 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:29.2
occ:1.00
NE2 A:HIS44 2.0 21.4 1.0
O A:HOH704 2.1 28.9 1.0
ND1 A:HIS40 2.1 25.2 1.0
O A:HOH536 2.1 25.2 1.0
O A:HOH513 2.2 16.9 1.0
CE1 A:HIS44 2.9 28.2 1.0
CE1 A:HIS40 3.0 25.6 1.0
CG A:HIS40 3.1 25.5 1.0
CD2 A:HIS44 3.1 19.2 1.0
CB A:HIS40 3.5 23.8 1.0
O A:HOH584 4.0 25.3 1.0
ND1 A:HIS44 4.1 28.5 1.0
NE2 A:HIS40 4.1 32.5 1.0
CD2 A:HIS40 4.2 26.0 1.0
O A:HOH642 4.2 35.9 1.0
CG A:HIS44 4.2 18.0 1.0
CA A:HIS40 4.4 19.0 1.0
C A:HIS40 4.6 13.0 1.0
O A:HIS40 4.7 16.3 1.0
NE A:ARG75 4.8 37.5 1.0

Zinc binding site 3 out of 7 in 4dlm

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Zinc binding site 3 out of 7 in the Crystal Structure of An Amidohydrolase (COG3618) From Burkholderia Multivorans (Target Efi-500235) with Bound Zn, Space Group P212121


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 An Amidohydrolase (COG3618) From Burkholderia Multivorans (Target Efi-500235) with Bound Zn, Space Group P212121 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:24.1
occ:1.00
NE2 A:HIS222 2.0 17.9 1.0
O A:HOH712 2.0 23.6 1.0
O A:HOH711 2.1 18.5 1.0
O A:HOH713 2.2 18.6 1.0
CE1 A:HIS222 3.0 14.5 1.0
CD2 A:HIS222 3.0 14.3 1.0
ND1 A:HIS222 4.1 14.7 1.0
CG A:HIS222 4.2 18.8 1.0
O A:PHE175 4.2 20.8 1.0
O A:HOH575 4.4 21.2 1.0
C A:PHE175 4.9 22.0 1.0
CA A:ASP176 5.0 35.0 1.0

Zinc binding site 4 out of 7 in 4dlm

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Zinc binding site 4 out of 7 in the Crystal Structure of An Amidohydrolase (COG3618) From Burkholderia Multivorans (Target Efi-500235) with Bound Zn, Space Group P212121


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 An Amidohydrolase (COG3618) From Burkholderia Multivorans (Target Efi-500235) with Bound Zn, Space Group P212121 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn404

b:41.3
occ:1.00
OD1 A:ASP135 2.0 37.2 1.0
O A:HOH701 2.1 37.5 1.0
O A:HOH598 2.1 50.4 1.0
O A:HOH702 2.1 39.4 1.0
O A:HOH643 2.2 30.9 1.0
O A:HOH569 3.0 35.3 1.0
CG A:ASP135 3.0 32.9 1.0
OD2 A:ASP135 3.4 38.5 1.0
O A:HOH674 3.9 43.1 1.0
O A:GLN132 4.0 23.8 1.0
ND1 A:HIS160 4.3 18.8 1.0
CB A:ASP135 4.4 26.9 1.0
O A:ALA159 4.5 32.0 1.0
CA A:ASP135 4.6 20.7 1.0
N A:ASP135 4.7 23.4 1.0
O A:ALA133 4.7 24.1 1.0
CE1 A:HIS160 4.9 18.0 1.0

Zinc binding site 5 out of 7 in 4dlm

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Zinc binding site 5 out of 7 in the Crystal Structure of An Amidohydrolase (COG3618) From Burkholderia Multivorans (Target Efi-500235) with Bound Zn, Space Group P212121


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 An Amidohydrolase (COG3618) From Burkholderia Multivorans (Target Efi-500235) with Bound Zn, Space Group P212121 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn405

b:70.9
occ:1.00
OD2 A:ASP158 2.1 37.5 1.0
CG A:ASP158 2.9 27.2 1.0
OD1 A:ASP158 3.0 29.9 1.0
CB A:ASP158 4.3 22.3 1.0
O A:ALA155 4.9 25.2 1.0

Zinc binding site 6 out of 7 in 4dlm

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Zinc binding site 6 out of 7 in the Crystal Structure of An Amidohydrolase (COG3618) From Burkholderia Multivorans (Target Efi-500235) with Bound Zn, Space Group P212121


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 An Amidohydrolase (COG3618) From Burkholderia Multivorans (Target Efi-500235) with Bound Zn, Space Group P212121 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn406

b:72.3
occ:1.00
OE1 A:GLU191 2.1 53.0 1.0
OE2 A:GLU191 2.1 56.0 1.0
CD A:GLU191 2.4 49.4 1.0
CG A:GLU191 3.8 38.0 1.0
O A:HOH559 4.2 24.9 1.0
CB A:GLU191 4.8 25.0 1.0

Zinc binding site 7 out of 7 in 4dlm

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Zinc binding site 7 out of 7 in the Crystal Structure of An Amidohydrolase (COG3618) From Burkholderia Multivorans (Target Efi-500235) with Bound Zn, Space Group P212121


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 An Amidohydrolase (COG3618) From Burkholderia Multivorans (Target Efi-500235) with Bound Zn, Space Group P212121 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn407

b:66.9
occ:1.00
OD2 A:ASP228 2.0 23.4 1.0
NH2 A:ARG268 2.1 16.8 0.4
OE2 A:GLU224 2.5 23.0 0.5
CG A:ASP228 3.0 16.9 1.0
CD A:GLU224 3.0 23.9 0.5
CZ A:ARG268 3.0 17.2 0.4
OD1 A:ASP228 3.3 15.7 1.0
NE A:ARG268 3.4 13.1 0.4
CG A:GLU224 3.4 22.8 0.5
OE1 A:GLU224 3.7 24.4 0.5
NH1 A:ARG268 4.1 14.6 0.4
CB A:ASP228 4.3 12.2 1.0
O A:GLU224 4.4 16.3 0.5
O A:HOH693 4.5 39.2 1.0
O A:GLU224 4.6 15.0 0.5
CB A:GLU224 4.7 20.0 0.5
CD A:ARG268 4.8 20.7 0.4
CB A:GLU224 4.8 20.8 0.5
C A:GLU224 4.8 16.7 0.5
C A:GLU224 4.9 16.7 0.5

Reference:

M.W.Vetting, R.Toro, R.Bhosle, R.D.Seidel, B.Hillerich, E.Washington, A.Scott Glenn, S.Chowdhury, B.Evans, J.Hammonds, N.F.Al Obaidi, W.D.Zencheck, H.J.Imker, J.A.Gerlt, F.M.Raushel, S.C.Almo, Enzyme Function Initiative (Efi). Crystal Structure of An Amidohydrolase (COG3618) From Burkholderia Multivorans (Target Efi-500235) with Bound Zn, Space Group P212121 To Be Published.
Page generated: Wed Dec 16 05:11:37 2020

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