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Zinc in PDB 5mxz: KUSTC0563 Y40F Mutant

Protein crystallography data

The structure of KUSTC0563 Y40F Mutant, PDB code: 5mxz was solved by A.Mohd, T.Barends, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.90 / 1.90
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 47.520, 47.520, 99.780, 90.00, 90.00, 90.00
R / Rfree (%) 20.1 / 22.5

Other elements in 5mxz:

The structure of KUSTC0563 Y40F Mutant also contains other interesting chemical elements:

Iron (Fe) 1 atom

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Zinc atom in the KUSTC0563 Y40F Mutant (pdb code 5mxz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 11 binding sites of Zinc where determined in the KUSTC0563 Y40F Mutant, PDB code: 5mxz:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 11 in 5mxz

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Zinc binding site 1 out of 11 in the KUSTC0563 Y40F Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of KUSTC0563 Y40F Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:27.6
occ:1.00
O A:HOH315 2.0 29.6 1.0
O A:HOH307 2.0 26.7 1.0
O1D A:HEC200 2.2 26.0 1.0
CGD A:HEC200 3.2 25.6 1.0
O2D A:HEC200 3.5 25.0 1.0
OG1 A:THR87 3.8 26.9 1.0
OE1 A:GLN82 4.0 24.7 1.0
O A:HOH317 4.2 39.6 1.0
O A:HOH360 4.2 44.3 1.0
CG2 A:THR87 4.5 26.0 1.0
NH1 A:ARG78 4.5 26.6 1.0
CBD A:HEC200 4.5 24.5 1.0
CB A:THR87 4.8 26.9 1.0
CD A:GLN82 4.9 23.8 1.0

Zinc binding site 2 out of 11 in 5mxz

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Zinc binding site 2 out of 11 in the KUSTC0563 Y40F Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of KUSTC0563 Y40F Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn202

b:72.1
occ:1.00
OD2 A:ASP67 2.6 42.6 1.0
OE1 A:GLU69 2.7 39.5 0.5
OD1 A:ASP67 3.0 36.9 1.0
CG A:ASP67 3.2 37.6 1.0
CD A:GLU69 3.2 39.0 0.5
OE2 A:GLU69 3.7 39.5 0.5
CB A:GLU69 3.9 36.6 0.5
CG A:GLU69 4.0 37.6 0.5
CB A:GLU69 4.0 37.5 0.5
OE1 A:GLU69 4.3 42.8 0.5
CB A:ASP67 4.6 35.7 1.0
N A:GLU69 4.7 35.0 1.0
O A:HOH302 4.8 56.3 1.0
CD A:GLU69 4.9 40.9 0.5
CA A:GLU69 4.9 35.1 0.5
CA A:GLU69 5.0 35.5 0.5

Zinc binding site 3 out of 11 in 5mxz

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Zinc binding site 3 out of 11 in the KUSTC0563 Y40F Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of KUSTC0563 Y40F Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn203

b:49.3
occ:1.00
OE2 A:GLU77 2.1 41.9 1.0
CD A:GLU77 2.7 40.9 1.0
OE1 A:GLU77 2.7 44.3 1.0
ZN A:ZN211 2.8 0.0 1.0
CG A:GLU77 4.1 36.9 1.0
CB A:GLU77 4.9 32.0 1.0

Zinc binding site 4 out of 11 in 5mxz

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Zinc binding site 4 out of 11 in the KUSTC0563 Y40F Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of KUSTC0563 Y40F Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn204

b:30.9
occ:0.50
O A:ACT217 2.0 45.3 1.0
OD2 A:ASP76 2.2 33.3 1.0
OD1 A:ASP76 2.6 32.1 1.0
CG A:ASP76 2.7 31.8 1.0
C A:ACT217 2.9 45.3 1.0
OXT A:ACT217 3.2 47.1 1.0
O A:HOH310 3.9 26.6 1.0
CB A:ASP76 4.2 29.8 1.0
NE A:ARG111 4.3 27.7 1.0
NH2 A:ARG111 4.3 25.8 1.0
CH3 A:ACT217 4.3 46.5 1.0
CZ A:ARG111 4.7 26.7 1.0
CG1 A:VAL107 5.0 25.7 1.0

Zinc binding site 5 out of 11 in 5mxz

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Zinc binding site 5 out of 11 in the KUSTC0563 Y40F Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of KUSTC0563 Y40F Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn205

b:38.4
occ:1.00
OE2 A:GLU58 1.9 40.5 1.0
O A:HOH346 2.0 40.3 1.0
CD A:GLU58 2.8 37.2 1.0
OE1 A:GLU58 3.1 38.6 1.0
CG A:GLU58 4.2 35.0 1.0

Zinc binding site 6 out of 11 in 5mxz

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Zinc binding site 6 out of 11 in the KUSTC0563 Y40F Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of KUSTC0563 Y40F Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn206

b:97.5
occ:1.00
OE2 A:GLU81 2.5 31.5 1.0
OE1 A:GLU81 3.0 31.5 1.0
CD A:GLU81 3.2 30.6 1.0
O A:HOH345 3.3 44.5 1.0
CG A:GLU81 4.7 28.8 1.0
NE A:ARG78 4.8 26.6 1.0
O A:HOH319 5.0 39.7 1.0
NH2 A:ARG78 5.0 26.6 1.0

Zinc binding site 7 out of 11 in 5mxz

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Zinc binding site 7 out of 11 in the KUSTC0563 Y40F Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of KUSTC0563 Y40F Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn207

b:0.6
occ:1.00
ND1 A:HIS42 2.8 40.1 1.0
O A:HOH333 3.2 43.5 1.0
CE1 A:HIS42 3.6 41.0 1.0
CG A:HIS42 3.8 39.5 1.0
CA A:HIS42 3.9 35.6 1.0
O A:GLN41 4.0 38.6 1.0
CB A:HIS42 4.0 36.6 1.0
CE2 A:PHE94 4.2 26.3 1.0
O A:HIS42 4.4 32.1 1.0
C A:HIS42 4.7 32.8 1.0
C A:GLN41 4.7 39.2 1.0
N A:HIS42 4.8 36.2 1.0
NE2 A:HIS42 4.8 40.9 1.0
CD2 A:HIS42 4.9 40.1 1.0
CZ A:PHE94 5.0 25.2 1.0

Zinc binding site 8 out of 11 in 5mxz

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Zinc binding site 8 out of 11 in the KUSTC0563 Y40F Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of KUSTC0563 Y40F Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn208

b:81.8
occ:1.00
NE2 A:HIS42 2.4 40.9 1.0
OE1 A:GLN41 2.9 54.6 1.0
CE1 A:HIS42 3.0 41.0 1.0
CD2 A:HIS42 3.5 40.1 1.0
CD A:GLN41 3.8 52.6 1.0
ND1 A:HIS42 4.2 40.1 1.0
CB A:GLN41 4.4 43.7 1.0
CG A:HIS42 4.5 39.5 1.0
NE2 A:GLN41 4.5 54.3 1.0
CG A:GLN41 4.6 48.5 1.0
CD2 A:LEU38 4.6 34.0 1.0
O2 A:EDO214 4.7 58.5 1.0

Zinc binding site 9 out of 11 in 5mxz

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Zinc binding site 9 out of 11 in the KUSTC0563 Y40F Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of KUSTC0563 Y40F Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn209

b:0.4
occ:1.00
O A:HOH352 2.3 55.2 1.0
OD2 A:ASP34 2.9 50.5 1.0
OD1 A:ASP34 3.4 49.0 1.0
CG A:ASP34 3.5 48.9 1.0
CB A:MET36 4.3 39.4 1.0
CG A:MET36 4.8 41.8 1.0

Zinc binding site 10 out of 11 in 5mxz

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Zinc binding site 10 out of 11 in the KUSTC0563 Y40F Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of KUSTC0563 Y40F Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn210

b:76.5
occ:0.50
O A:HOH321 2.8 28.8 1.0
C A:GLY51 3.0 42.3 1.0
N A:ASN52 3.0 40.1 1.0
O A:GLY48 3.2 42.4 1.0
CA A:GLY51 3.3 43.1 1.0
O A:GLY51 3.4 42.0 1.0
CD2 A:PHE65 3.4 28.7 1.0
C A:ASN52 3.5 35.9 1.0
O A:ASN52 3.6 36.6 1.0
CA A:ASN52 3.7 38.2 1.0
CB A:HIS47 3.7 28.2 1.0
O2 A:EDO212 3.7 49.9 1.0
N A:GLY48 3.8 36.6 1.0
CG A:PHE65 3.9 28.3 1.0
CA A:HIS47 3.9 30.7 1.0
N A:GLY51 3.9 42.9 1.0
C A:HIS47 3.9 34.3 1.0
N A:PRO53 4.0 32.9 1.0
N A:PHE65 4.0 28.7 1.0
CE2 A:PHE65 4.0 28.2 1.0
CB A:PHE65 4.0 28.8 1.0
C A:GLY48 4.3 41.8 1.0
ND1 A:HIS47 4.5 26.1 1.0
CA A:GLY48 4.6 38.3 1.0
CG A:HIS47 4.6 26.9 1.0
O A:HIS47 4.6 37.3 1.0
CA A:PRO53 4.6 32.7 1.0
CD A:PRO53 4.7 32.4 1.0
CA A:PHE65 4.7 29.3 1.0
CD1 A:PHE65 4.8 28.2 1.0
O A:ARG63 4.9 29.7 1.0
CZ A:PHE65 5.0 27.4 1.0
C A:LYS64 5.0 28.9 1.0

Reference:

A.Mohd, T.Barends. Structure and Function of the C-Type Cytochrome KUSTC0563 From Kuenenia Stuttgartiensis To Be Published.
Page generated: Wed Dec 16 06:33:55 2020

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