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Zinc in PDB 1zzm: Crystal Structure of Yjjv, Tatd Homolog From Escherichia Coli K12, at 1.8 A Resolution

Protein crystallography data

The structure of Crystal Structure of Yjjv, Tatd Homolog From Escherichia Coli K12, at 1.8 A Resolution, PDB code: 1zzm was solved by V.N.Malashkevich, D.F.Xiang, F.M.Raushel, S.C.Almo, S.K.Burley, New Yorksgx Research Center For Structural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.87 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 47.186, 45.007, 57.824, 90.00, 100.75, 90.00
R / Rfree (%) 17.1 / 23.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Yjjv, Tatd Homolog From Escherichia Coli K12, at 1.8 A Resolution (pdb code 1zzm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Yjjv, Tatd Homolog From Escherichia Coli K12, at 1.8 A Resolution, PDB code: 1zzm:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1zzm

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Zinc binding site 1 out of 4 in the Crystal Structure of Yjjv, Tatd Homolog From Escherichia Coli K12, at 1.8 A Resolution


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 Yjjv, Tatd Homolog From Escherichia Coli K12, at 1.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:12.4
occ:1.00
NE2 A:HIS11 2.0 11.3 1.0
OE1 A:GLU97 2.0 13.6 1.0
O A:HOH767 2.0 10.8 1.0
NE2 A:HIS9 2.1 5.4 1.0
OD1 A:ASP207 2.7 16.3 1.0
CD A:GLU97 2.9 9.4 1.0
CE1 A:HIS11 2.9 8.6 1.0
CD2 A:HIS11 3.0 12.8 1.0
CD2 A:HIS9 3.1 7.2 1.0
OE2 A:GLU97 3.1 10.5 1.0
CE1 A:HIS9 3.1 10.4 1.0
ZN A:ZN402 3.2 12.7 1.0
CG A:ASP207 3.6 16.1 1.0
NE2 A:HIS157 3.8 10.6 1.0
O A:HOH854 3.8 12.7 1.0
OD2 A:ASP207 4.0 19.0 1.0
CE1 A:HIS157 4.0 10.4 1.0
ND1 A:HIS11 4.1 10.0 1.0
CG A:HIS11 4.2 7.7 1.0
ND1 A:HIS9 4.2 7.2 1.0
CG A:HIS9 4.2 7.0 1.0
CG A:GLU97 4.3 13.9 1.0
NE2 A:HIS66 4.4 17.8 1.0
CD2 A:HIS157 4.5 8.8 1.0
O A:HOH791 4.5 13.4 1.0
CD2 A:HIS66 4.6 15.2 1.0
CG A:PRO39 4.7 12.3 1.0
ND1 A:HIS157 4.8 9.7 1.0
C6 A:P33501 4.8 32.8 1.0
CB A:ASP207 4.9 16.6 1.0
CB A:GLU97 4.9 10.9 1.0
C5 A:P33501 4.9 31.0 1.0

Zinc binding site 2 out of 4 in 1zzm

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Zinc binding site 2 out of 4 in the Crystal Structure of Yjjv, Tatd Homolog From Escherichia Coli K12, at 1.8 A Resolution


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 Yjjv, Tatd Homolog From Escherichia Coli K12, at 1.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:12.7
occ:1.00
O A:HOH767 2.0 10.8 1.0
ND1 A:HIS133 2.0 10.3 1.0
NE2 A:HIS157 2.1 10.6 1.0
OE2 A:GLU97 2.1 10.5 1.0
O A:HOH791 2.4 13.4 1.0
CE1 A:HIS133 2.9 13.3 1.0
CE1 A:HIS157 3.1 10.4 1.0
CD2 A:HIS157 3.1 8.8 1.0
CG A:HIS133 3.1 11.3 1.0
CD A:GLU97 3.2 9.4 1.0
ZN A:ZN401 3.2 12.4 1.0
CB A:HIS133 3.6 9.0 1.0
OE1 A:GLU97 3.6 13.6 1.0
O A:HOH854 3.7 12.7 1.0
NE2 A:HIS66 3.8 17.8 1.0
O A:HOH683 4.0 25.5 1.0
O A:HOH527 4.1 18.6 1.0
NE2 A:HIS133 4.1 11.4 1.0
NE2 A:HIS9 4.1 5.4 1.0
OD2 A:ASP207 4.2 19.0 1.0
ND1 A:HIS157 4.2 9.7 1.0
CA A:HIS133 4.2 10.4 1.0
CD2 A:HIS133 4.2 10.3 1.0
CG A:HIS157 4.2 8.9 1.0
CE1 A:HIS9 4.4 10.4 1.0
CG A:GLU97 4.5 13.9 1.0
OD1 A:ASP207 4.5 16.3 1.0
CE1 A:HIS66 4.5 15.9 1.0
CG A:ASP207 4.6 16.1 1.0
CD2 A:HIS66 4.6 15.2 1.0

Zinc binding site 3 out of 4 in 1zzm

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Zinc binding site 3 out of 4 in the Crystal Structure of Yjjv, Tatd Homolog From Escherichia Coli K12, at 1.8 A Resolution


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 Yjjv, Tatd Homolog From Escherichia Coli K12, at 1.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:14.4
occ:1.00
OD2 A:ASP117 1.9 13.4 1.0
NE2 A:HIS148 2.0 14.6 1.0
ND1 A:HIS144 2.2 15.2 1.0
CG A:ASP117 2.6 12.5 1.0
OD1 A:ASP117 2.6 14.6 1.0
CD2 A:HIS148 2.9 14.4 1.0
CE1 A:HIS144 3.0 16.5 1.0
CE1 A:HIS148 3.0 19.2 1.0
CG A:HIS144 3.2 15.3 1.0
CB A:HIS144 3.7 12.5 1.0
O A:HOH778 4.0 50.5 1.0
CB A:ASP117 4.0 11.3 1.0
CA A:HIS144 4.1 13.3 1.0
CG A:HIS148 4.1 16.4 1.0
ND1 A:HIS148 4.1 18.2 1.0
NE2 A:HIS144 4.2 15.3 1.0
CD2 A:HIS144 4.3 13.4 1.0
O A:HIS144 4.8 12.2 1.0
C A:HIS144 4.9 13.8 1.0
O A:HOH628 4.9 30.0 1.0

Zinc binding site 4 out of 4 in 1zzm

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Zinc binding site 4 out of 4 in the Crystal Structure of Yjjv, Tatd Homolog From Escherichia Coli K12, at 1.8 A Resolution


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 Yjjv, Tatd Homolog From Escherichia Coli K12, at 1.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn404

b:44.6
occ:1.00
N A:MET1 2.2 36.3 1.0
O A:HOH848 2.4 32.4 1.0
O A:HOH553 2.5 23.2 1.0
CA A:MET1 3.2 35.6 1.0
C A:MET1 3.4 34.2 1.0
O A:MET1 3.5 31.8 1.0
O A:HOH729 3.9 35.2 1.0
N A:ILE2 4.3 31.4 1.0
CB A:MET1 4.5 36.9 1.0
O A:HOH864 4.9 45.0 1.0

Reference:

V.N.Malashkevich, D.F.Xiang, F.M.Raushel, S.C.Almo. Crystal Structure of Yjjv, Tatd Homolog From Escherichia Coli K12, at 1.8 A Resolution To Be Published.
Page generated: Wed Dec 16 03:16:20 2020

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