Zinc in PDB 6wp2: The Crystal Structure of Apo Zinc-Bound Domain Swapped-Trimer Q108K:K40D:T53A:R58L:Q38F:Q4F:F57H Variant of Hcrbpii

Protein crystallography data

The structure of The Crystal Structure of Apo Zinc-Bound Domain Swapped-Trimer Q108K:K40D:T53A:R58L:Q38F:Q4F:F57H Variant of Hcrbpii, PDB code: 6wp2 was solved by A.Ghanbarpour, J.Geiger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.17 / 2.48
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.513, 74.451, 94.345, 90.00, 90.00, 90.00
R / Rfree (%) 22.2 / 31.2

Zinc Binding Sites:

The binding sites of Zinc atom in the The Crystal Structure of Apo Zinc-Bound Domain Swapped-Trimer Q108K:K40D:T53A:R58L:Q38F:Q4F:F57H Variant of Hcrbpii (pdb code 6wp2). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the The Crystal Structure of Apo Zinc-Bound Domain Swapped-Trimer Q108K:K40D:T53A:R58L:Q38F:Q4F:F57H Variant of Hcrbpii, PDB code: 6wp2:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 6wp2

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Zinc binding site 1 out of 6 in the The Crystal Structure of Apo Zinc-Bound Domain Swapped-Trimer Q108K:K40D:T53A:R58L:Q38F:Q4F:F57H Variant of Hcrbpii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Crystal Structure of Apo Zinc-Bound Domain Swapped-Trimer Q108K:K40D:T53A:R58L:Q38F:Q4F:F57H Variant of Hcrbpii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:49.0
occ:1.00
ZN A:ZN204 1.8 31.9 0.7
ZN A:ZN203 1.9 35.5 0.5
NE2 A:HIS57 2.2 43.5 0.7
NE2 B:HIS57 2.3 44.7 0.1
CE1 A:HIS57 2.4 45.5 0.3
NE2 A:HIS57 2.4 44.7 0.3
NE2 C:HIS57 2.5 41.0 0.5
NE2 B:HIS57 2.5 43.2 0.9
NE2 C:HIS57 2.6 40.7 0.5
CE1 B:HIS57 2.9 47.5 0.9
CE1 C:HIS57 2.9 44.9 0.5
CE1 A:HIS57 3.0 48.6 0.7
CE1 C:HIS57 3.0 43.6 0.5
CE1 B:HIS57 3.0 47.0 0.1
CD2 A:HIS57 3.3 40.5 0.7
CD2 B:HIS57 3.6 44.2 0.1
ND1 A:HIS57 3.6 48.6 0.3
CD2 C:HIS57 3.7 41.7 0.5
CD2 A:HIS57 3.7 44.8 0.3
CD2 B:HIS57 3.8 41.3 0.9
CD2 C:HIS57 3.8 41.3 0.5
ND1 A:HIS57 4.2 49.8 0.7
ND1 B:HIS57 4.2 50.2 0.9
ND1 C:HIS57 4.2 45.6 0.5
ND1 B:HIS57 4.3 49.2 0.1
ND1 C:HIS57 4.3 43.9 0.5
CG A:HIS57 4.3 48.4 0.3
CG A:HIS57 4.4 48.9 0.7
CG B:HIS57 4.5 49.1 0.1
CG2 A:ILE32 4.6 44.5 1.0
CG B:HIS57 4.6 50.0 0.9
CG C:HIS57 4.6 46.0 0.5
CG C:HIS57 4.7 46.3 0.5
CG2 C:ILE32 4.7 42.1 1.0
CD2 A:LEU36 4.8 46.9 1.0
CG2 B:ILE32 5.0 28.1 1.0

Zinc binding site 2 out of 6 in 6wp2

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Zinc binding site 2 out of 6 in the The Crystal Structure of Apo Zinc-Bound Domain Swapped-Trimer Q108K:K40D:T53A:R58L:Q38F:Q4F:F57H Variant of Hcrbpii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Crystal Structure of Apo Zinc-Bound Domain Swapped-Trimer Q108K:K40D:T53A:R58L:Q38F:Q4F:F57H Variant of Hcrbpii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn202

b:56.6
occ:1.00
CD2 B:HIS57 4.0 41.3 0.9
CD2 A:HIS57 4.2 40.5 0.7
CD2 C:HIS57 4.2 41.3 0.5
CA B:THR56 4.2 43.4 1.0
N A:HIS57 4.3 62.0 1.0
CD2 A:HIS57 4.3 44.8 0.3
ZN A:ZN203 4.4 35.5 0.5
CD2 C:HIS57 4.4 41.7 0.5
CD2 B:HIS57 4.4 44.2 0.1
OG1 A:THR56 4.6 66.2 1.0
CA C:THR56 4.6 50.3 1.0
CA A:THR56 4.6 52.2 1.0
N B:HIS57 4.6 50.5 1.0
CG A:HIS57 4.6 48.4 0.3
CG2 C:THR56 4.7 40.6 1.0
CB C:THR56 4.7 47.6 1.0
N C:HIS57 4.8 50.4 1.0
N B:THR56 4.8 57.4 1.0
CB A:HIS57 4.8 49.4 0.3
NE2 B:HIS57 4.8 43.2 0.9
CB A:HIS57 4.8 49.4 0.7
CG A:HIS57 4.9 48.9 0.7
C B:THR56 4.9 55.7 1.0
CB B:THR56 4.9 56.5 1.0
C A:THR56 4.9 51.5 1.0
O C:SER55 4.9 40.1 1.0
NE2 C:HIS57 5.0 40.7 0.5

Zinc binding site 3 out of 6 in 6wp2

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Zinc binding site 3 out of 6 in the The Crystal Structure of Apo Zinc-Bound Domain Swapped-Trimer Q108K:K40D:T53A:R58L:Q38F:Q4F:F57H Variant of Hcrbpii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Crystal Structure of Apo Zinc-Bound Domain Swapped-Trimer Q108K:K40D:T53A:R58L:Q38F:Q4F:F57H Variant of Hcrbpii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn203

b:35.5
occ:0.49
NE2 B:HIS57 1.8 43.2 0.9
NE2 C:HIS57 1.9 41.0 0.5
NE2 A:HIS57 1.9 44.7 0.3
ZN A:ZN201 1.9 49.0 1.0
NE2 A:HIS57 1.9 43.5 0.7
NE2 C:HIS57 1.9 40.7 0.5
NE2 B:HIS57 2.0 44.7 0.1
CD2 A:HIS57 2.2 40.5 0.7
CE1 A:HIS57 2.3 45.5 0.3
CD2 B:HIS57 2.5 44.2 0.1
CD2 B:HIS57 2.6 41.3 0.9
CD2 C:HIS57 2.7 41.3 0.5
CD2 C:HIS57 2.7 41.7 0.5
CD2 A:HIS57 2.7 44.8 0.3
CE1 C:HIS57 2.9 43.6 0.5
CE1 B:HIS57 2.9 47.5 0.9
CE1 C:HIS57 3.0 44.9 0.5
ND1 A:HIS57 3.2 48.6 0.3
CE1 B:HIS57 3.2 47.0 0.1
CE1 A:HIS57 3.2 48.6 0.7
CG A:HIS57 3.4 48.4 0.3
CG A:HIS57 3.5 48.9 0.7
ZN A:ZN204 3.7 31.9 0.7
CG B:HIS57 3.8 49.1 0.1
CG B:HIS57 3.8 50.0 0.9
CG C:HIS57 3.8 46.0 0.5
CG C:HIS57 3.9 46.3 0.5
ND1 C:HIS57 3.9 43.9 0.5
ND1 B:HIS57 3.9 50.2 0.9
ND1 A:HIS57 4.0 49.8 0.7
ND1 C:HIS57 4.0 45.6 0.5
ND1 B:HIS57 4.1 49.2 0.1
ZN A:ZN202 4.4 56.6 1.0
CD2 A:LEU36 4.7 46.9 1.0
CD2 B:LEU36 4.7 46.4 1.0
CB A:HIS57 4.8 49.4 0.3
CB A:HIS57 4.8 49.4 0.7

Zinc binding site 4 out of 6 in 6wp2

Go back to Zinc Binding Sites List in 6wp2
Zinc binding site 4 out of 6 in the The Crystal Structure of Apo Zinc-Bound Domain Swapped-Trimer Q108K:K40D:T53A:R58L:Q38F:Q4F:F57H Variant of Hcrbpii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Crystal Structure of Apo Zinc-Bound Domain Swapped-Trimer Q108K:K40D:T53A:R58L:Q38F:Q4F:F57H Variant of Hcrbpii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn204

b:31.9
occ:0.67
ZN A:ZN201 1.8 49.0 1.0
CG2 A:ILE32 3.5 44.5 1.0
CE1 A:HIS57 3.5 45.5 0.3
NE2 A:HIS57 3.6 43.5 0.7
NE2 B:HIS57 3.7 44.7 0.1
CG2 C:ILE32 3.7 42.1 1.0
ZN A:ZN203 3.7 35.5 0.5
CE1 B:HIS57 3.8 47.0 0.1
CE1 A:HIS57 3.8 48.6 0.7
CE1 C:HIS57 3.8 44.9 0.5
CE1 B:HIS57 3.8 47.5 0.9
NE2 A:HIS57 3.8 44.7 0.3
NE2 C:HIS57 3.9 41.0 0.5
NE2 B:HIS57 4.0 43.2 0.9
CE1 C:HIS57 4.0 43.6 0.5
NE2 C:HIS57 4.0 40.7 0.5
CG2 B:ILE32 4.1 28.1 1.0
CG1 B:ILE32 4.2 39.0 1.0
CB A:ILE32 4.4 53.9 1.0
CG1 C:ILE32 4.4 48.4 1.0
CG1 A:ILE32 4.4 50.3 1.0
CB C:ILE32 4.6 45.2 1.0
CB B:ILE32 4.7 41.4 1.0
CA A:ILE32 4.7 43.4 1.0
ND1 A:HIS57 4.8 48.6 0.3
CD2 A:HIS57 4.9 40.5 0.7

Zinc binding site 5 out of 6 in 6wp2

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Zinc binding site 5 out of 6 in the The Crystal Structure of Apo Zinc-Bound Domain Swapped-Trimer Q108K:K40D:T53A:R58L:Q38F:Q4F:F57H Variant of Hcrbpii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of The Crystal Structure of Apo Zinc-Bound Domain Swapped-Trimer Q108K:K40D:T53A:R58L:Q38F:Q4F:F57H Variant of Hcrbpii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn205

b:68.5
occ:1.00
CG A:MET10 3.4 42.5 1.0
SD A:MET10 3.6 55.7 1.0
C A:GLU11 3.9 50.5 1.0
N A:SER12 3.9 52.3 1.0
CG2 A:THR37 4.2 58.5 1.0
CA A:GLU11 4.2 51.3 1.0
O A:GLU11 4.3 52.3 1.0
N A:GLU11 4.4 57.5 1.0
CA A:SER12 4.4 47.4 1.0
C A:SER12 4.5 50.5 1.0
C A:MET10 4.5 56.7 1.0
CB A:MET10 4.5 45.6 1.0
CB A:ASN13 4.6 42.8 1.0
O A:MET10 4.6 56.5 1.0
OG1 A:THR37 4.7 57.8 1.0
N A:ASN13 4.7 48.4 1.0
O A:SER12 4.9 44.9 1.0
CB A:THR37 4.9 42.6 1.0

Zinc binding site 6 out of 6 in 6wp2

Go back to Zinc Binding Sites List in 6wp2
Zinc binding site 6 out of 6 in the The Crystal Structure of Apo Zinc-Bound Domain Swapped-Trimer Q108K:K40D:T53A:R58L:Q38F:Q4F:F57H Variant of Hcrbpii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of The Crystal Structure of Apo Zinc-Bound Domain Swapped-Trimer Q108K:K40D:T53A:R58L:Q38F:Q4F:F57H Variant of Hcrbpii within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn201

b:51.5
occ:1.00
CB A:ALA28 4.1 40.7 1.0
CD2 C:PHE27 4.2 63.7 1.0
CB B:ALA28 4.3 37.0 1.0
CB C:ALA28 4.3 43.9 1.0
CD2 B:PHE27 4.5 44.7 1.0
CD2 A:PHE27 4.7 52.5 1.0
CE2 C:PHE27 4.7 54.0 1.0
N A:ALA28 4.8 48.6 1.0
CA A:ALA28 4.8 46.4 1.0
N C:ALA28 4.9 40.7 1.0
N B:ALA28 4.9 45.9 1.0
CA C:ALA28 4.9 46.0 1.0
CA B:ALA28 4.9 48.0 1.0

Reference:

A.Ghanbarpour, J.Geiger. The Crystal Structure of Apo Zinc-Bound Domain Swapped Trimer Q108K:K40D:T53A:R58L:Q38F:Q4F:F57H Variant of Hcrbpii To Be Published.
Page generated: Wed Dec 16 13:06:13 2020

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