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Zinc in PDB 7ljh: Structure of Poly(Aspartic Acid) Hydrolase PAHZ2 with Zn+2 Bound

Protein crystallography data

The structure of Structure of Poly(Aspartic Acid) Hydrolase PAHZ2 with Zn+2 Bound, PDB code: 7ljh was solved by C.A.Brambley, T.J.Yared, M.Gonzalez, A.L.Jansch, J.R.Wallen, M.H.Weiland, J.M.Miller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 117.44 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 48.399, 146.174, 197.238, 90, 90, 90
R / Rfree (%) 18.5 / 21.3

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 28;

Binding sites:

The binding sites of Zinc atom in the Structure of Poly(Aspartic Acid) Hydrolase PAHZ2 with Zn+2 Bound (pdb code 7ljh). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 28 binding sites of Zinc where determined in the Structure of Poly(Aspartic Acid) Hydrolase PAHZ2 with Zn+2 Bound, PDB code: 7ljh:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 28 in 7ljh

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Zinc binding site 1 out of 28 in the Structure of Poly(Aspartic Acid) Hydrolase PAHZ2 with Zn+2 Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Poly(Aspartic Acid) Hydrolase PAHZ2 with Zn+2 Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:103.5
occ:0.83
OD1 A:ASP160 2.3 66.2 1.0
O A:HOH692 2.5 41.2 1.0
O A:HOH693 3.0 65.1 1.0
CG A:ASP160 3.4 75.2 1.0
O A:GLY157 3.5 65.5 1.0
NE A:ARG316 3.7 62.6 1.0
OD2 A:ASP160 3.7 80.8 1.0
NH1 A:ARG200 4.1 53.7 1.0
C A:GLY157 4.3 73.7 1.0
CA A:GLY314 4.3 43.2 1.0
CD A:ARG316 4.4 48.5 1.0
N A:ASP315 4.6 45.5 1.0
CA A:SER158 4.6 68.5 1.0
NH2 A:ARG316 4.6 48.4 1.0
CG A:ARG316 4.7 61.5 1.0
CZ A:ARG316 4.7 59.7 1.0
CB A:ASP160 4.7 62.0 1.0
CD A:ARG200 4.8 50.0 1.0
N A:SER158 4.8 60.0 1.0
CZ A:ARG200 4.8 61.6 1.0
C A:GLY314 4.9 57.5 1.0
CA A:ASP160 4.9 60.2 1.0

Zinc binding site 2 out of 28 in 7ljh

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Zinc binding site 2 out of 28 in the Structure of Poly(Aspartic Acid) Hydrolase PAHZ2 with Zn+2 Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Poly(Aspartic Acid) Hydrolase PAHZ2 with Zn+2 Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:106.6
occ:0.78
O A:HOH689 2.2 50.1 1.0
ND1 A:HIS211 2.3 100.0 1.0
O A:HOH685 2.4 58.9 1.0
CE1 A:HIS211 3.2 83.9 1.0
CG A:HIS211 3.3 101.1 1.0
CB A:HIS211 3.6 82.9 1.0
CA A:GLY214 3.9 66.1 1.0
N A:GLY214 4.2 62.7 1.0
NE2 A:HIS211 4.3 91.9 1.0
CD2 A:HIS211 4.4 101.2 1.0
C A:GLY214 4.9 73.4 1.0

Zinc binding site 3 out of 28 in 7ljh

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Zinc binding site 3 out of 28 in the Structure of Poly(Aspartic Acid) Hydrolase PAHZ2 with Zn+2 Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Poly(Aspartic Acid) Hydrolase PAHZ2 with Zn+2 Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:56.4
occ:1.00
O A:HOH606 2.0 65.5 1.0
OD1 A:ASP28 2.1 76.9 1.0
O A:ARG25 2.6 58.4 1.0
CG A:ASP28 2.7 76.4 1.0
OD2 A:ASP28 2.8 87.0 1.0
C A:ARG25 3.8 76.6 1.0
CB A:ASP28 4.2 69.0 1.0
CA A:ASP26 4.5 69.5 1.0
OD1 A:ASP26 4.6 71.8 1.0
N A:ASP26 4.6 76.2 1.0
CA A:ARG25 4.8 64.8 1.0
CG A:ARG25 4.8 61.7 1.0
N A:ASP28 4.9 61.3 1.0

Zinc binding site 4 out of 28 in 7ljh

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Zinc binding site 4 out of 28 in the Structure of Poly(Aspartic Acid) Hydrolase PAHZ2 with Zn+2 Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Poly(Aspartic Acid) Hydrolase PAHZ2 with Zn+2 Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn504

b:120.2
occ:0.60
OD2 A:ASP32 2.2 98.1 1.0
CG A:ASP32 3.1 91.7 1.0
OD1 A:ASP32 3.3 106.1 1.0
CB A:ASP32 4.5 77.6 1.0

Zinc binding site 5 out of 28 in 7ljh

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Zinc binding site 5 out of 28 in the Structure of Poly(Aspartic Acid) Hydrolase PAHZ2 with Zn+2 Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Poly(Aspartic Acid) Hydrolase PAHZ2 with Zn+2 Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn505

b:109.3
occ:0.58
O A:HOH700 2.4 70.2 1.0
OE1 A:GLU266 2.4 66.5 1.0
O A:HOH684 2.5 67.8 1.0
CD A:GLU266 3.2 59.2 1.0
OE2 A:GLU266 3.3 82.8 1.0
CG2 A:VAL249 4.4 46.7 1.0
CG A:GLU266 4.7 53.7 1.0
CD1 A:ILE313 4.8 39.8 1.0
CB A:VAL249 4.9 58.3 1.0
CG1 A:VAL249 4.9 37.4 1.0

Zinc binding site 6 out of 28 in 7ljh

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Zinc binding site 6 out of 28 in the Structure of Poly(Aspartic Acid) Hydrolase PAHZ2 with Zn+2 Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Poly(Aspartic Acid) Hydrolase PAHZ2 with Zn+2 Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn506

b:115.6
occ:0.72
OE2 A:GLU71 2.8 78.3 1.0
OE1 A:GLU71 2.9 74.5 1.0
CD A:GLU71 3.2 62.7 1.0
O A:HOH708 3.9 93.4 1.0
O A:HOH669 4.3 58.9 1.0
CG A:GLU71 4.7 58.0 1.0
NH1 A:ARG162 4.8 65.0 1.0

Zinc binding site 7 out of 28 in 7ljh

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Zinc binding site 7 out of 28 in the Structure of Poly(Aspartic Acid) Hydrolase PAHZ2 with Zn+2 Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of Poly(Aspartic Acid) Hydrolase PAHZ2 with Zn+2 Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn507

b:104.2
occ:0.53
OD2 A:ASP60 2.6 92.2 1.0
O A:HOH664 3.1 65.2 1.0
CG A:ASP60 3.6 88.0 1.0
CG A:MET57 3.8 69.9 1.0
O A:HOH666 3.8 64.6 1.0
CB A:ASP60 4.1 62.6 1.0
NZ A:LYS36 4.5 88.0 1.0
CA A:MET57 4.5 58.5 1.0
CB A:MET57 4.6 63.0 1.0
OD1 A:ASP60 4.7 87.5 1.0
O A:HOH611 4.8 74.9 1.0
N A:MET57 5.0 76.2 1.0
CE A:MET57 5.0 59.6 1.0
O A:GLU56 5.0 61.0 1.0

Zinc binding site 8 out of 28 in 7ljh

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Zinc binding site 8 out of 28 in the Structure of Poly(Aspartic Acid) Hydrolase PAHZ2 with Zn+2 Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of Poly(Aspartic Acid) Hydrolase PAHZ2 with Zn+2 Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn508

b:131.5
occ:0.67
OD2 A:ASP341 2.9 125.6 1.0
OD1 A:ASP341 3.6 114.3 1.0
CG A:ASP341 3.6 120.3 1.0

Zinc binding site 9 out of 28 in 7ljh

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Zinc binding site 9 out of 28 in the Structure of Poly(Aspartic Acid) Hydrolase PAHZ2 with Zn+2 Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structure of Poly(Aspartic Acid) Hydrolase PAHZ2 with Zn+2 Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn509

b:131.4
occ:0.64
O A:HOH616 4.0 55.3 1.0
OD2 A:ASP341 4.2 125.6 1.0
CB A:ASP341 4.4 84.0 1.0
CG A:ASP341 4.7 120.3 1.0
O A:PRO342 4.8 76.0 1.0

Zinc binding site 10 out of 28 in 7ljh

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Zinc binding site 10 out of 28 in the Structure of Poly(Aspartic Acid) Hydrolase PAHZ2 with Zn+2 Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Structure of Poly(Aspartic Acid) Hydrolase PAHZ2 with Zn+2 Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn510

b:142.6
occ:0.71
OE1 A:GLU17 2.7 120.8 1.0
OE2 A:GLU17 2.7 111.1 1.0
NZ A:LYS14 2.9 113.1 1.0
CD A:GLU17 3.1 105.7 1.0
CE A:LYS14 3.9 117.6 1.0
O A:LYS12 4.4 100.0 1.0
CG A:GLU17 4.6 94.6 1.0
CD A:LYS14 4.7 114.8 1.0

Reference:

C.A.Brambley, T.J.Yared, M.Gonzalez, A.L.Jansch, J.R.Wallen, M.H.Weiland, J.M.Miller. Sphingomonas Sp. Kt-1 PAHZ2 Structure Reveals A Role For Conformational Dynamics in Peptide Bond Hydrolysis. J.Phys.Chem.B V. 125 5722 2021.
ISSN: ISSN 1089-5647
PubMed: 34060838
DOI: 10.1021/ACS.JPCB.1C01216
Page generated: Fri Dec 17 11:50:30 2021

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