Zinc in PDB 6p9u: Crystal Structure of Human Thrombin Mutant W215A

Enzymatic activity of Crystal Structure of Human Thrombin Mutant W215A

All present enzymatic activity of Crystal Structure of Human Thrombin Mutant W215A:
3.4.21.5;

Protein crystallography data

The structure of Crystal Structure of Human Thrombin Mutant W215A, PDB code: 6p9u was solved by L.A.Pelc, S.K.Koester, Z.Chen, E.Di Cera, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.59 / 3.30
Space group P 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 136.320, 44.232, 136.187, 90.00, 90.04, 90.00
R / Rfree (%) 22.5 / 30.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Thrombin Mutant W215A (pdb code 6p9u). 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 Human Thrombin Mutant W215A, PDB code: 6p9u:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 6p9u

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Zinc binding site 1 out of 7 in the Crystal Structure of Human Thrombin Mutant W215A


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 Human Thrombin Mutant W215A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:62.5
occ:1.00
 NE2 B:HIS119 2.1 64.2 1.0
OD2 A:ASP1A 2.2 75.8 1.0
O B:HOH801 2.2 45.5 1.0
CE1 B:HIS119 3.0 65.8 1.0
CD2 B:HIS119 3.2 62.4 1.0
CG A:ASP1A 3.4 74.0 1.0
NZ A:LYS9 4.1 68.4 1.0
ND1 B:HIS119 4.1 66.4 1.0
CG B:HIS119 4.3 62.0 1.0
OD1 A:ASP1A 4.3 72.0 1.0
CB A:ASP1A 4.3 67.5 1.0
O A:ASP1A 4.5 53.1 1.0
CE A:LYS9 4.7 68.7 1.0

Zinc binding site 2 out of 7 in 6p9u

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Zinc binding site 2 out of 7 in the Crystal Structure of Human Thrombin Mutant W215A


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 Human Thrombin Mutant W215A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn101

b:68.4
occ:0.50
 CD H:GLU217 1.9 72.0 1.0
OE1 C:GLU14H 2.0 73.9 1.0
OE2 C:GLU14H 2.0 74.2 1.0
OE1 H:GLU217 2.0 70.8 1.0
CD C:GLU14H 2.1 81.2 1.0
OE2 H:GLU217 2.4 66.1 1.0
CG H:GLU217 2.6 73.7 1.0
CG C:GLU14H 3.4 84.7 1.0
CB H:GLU217 3.7 76.5 1.0
CA C:GLU14E 3.7 70.5 1.0
CB C:GLU14E 4.0 70.1 1.0
CB C:GLU14H 4.2 82.0 1.0
CG C:GLU14E 4.2 69.9 1.0
N C:GLU14E 4.4 66.1 1.0
O H:HOH801 4.7 22.2 1.0
O C:GLU14E 4.8 77.6 1.0
C C:GLU14E 4.8 70.7 1.0

Zinc binding site 3 out of 7 in 6p9u

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Zinc binding site 3 out of 7 in the Crystal Structure of Human Thrombin Mutant W215A


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 Human Thrombin Mutant W215A within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:56.9
occ:1.00
 OD2 C:ASP1A 2.0 64.1 1.0
NE2 D:HIS119 2.1 57.2 1.0
O D:HOH501 2.2 71.2 1.0
CE1 D:HIS119 2.9 62.2 1.0
CG C:ASP1A 3.2 69.3 1.0
CD2 D:HIS119 3.3 53.5 1.0
NZ C:LYS9 4.0 62.7 1.0
OD1 C:ASP1A 4.1 65.2 1.0
CB C:ASP1A 4.1 71.7 1.0
ND1 D:HIS119 4.1 60.8 1.0
CG D:HIS119 4.3 55.1 1.0
O C:ASP1A 4.7 65.1 1.0
CE C:LYS9 4.7 64.9 1.0
CD2 D:PHE114 4.8 60.9 1.0
CG C:PRO5 4.9 72.5 1.0

Zinc binding site 4 out of 7 in 6p9u

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Zinc binding site 4 out of 7 in the Crystal Structure of Human Thrombin Mutant W215A


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 Human Thrombin Mutant W215A within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn402

b:81.4
occ:0.50
 CD D:GLU217 1.9 77.6 1.0
OE2 D:GLU217 2.0 78.6 1.0
OE2 E:GLU14H 2.0 82.1 1.0
OE1 E:GLU14H 2.0 99.3 1.0
OE1 D:GLU217 2.0 68.4 1.0
CD E:GLU14H 2.3 90.6 1.0
CG D:GLU217 3.1 79.6 1.0
CG E:GLU14E 3.2 80.6 1.0
CD E:GLU14E 3.6 83.5 1.0
CB E:GLU14E 3.7 75.5 1.0
CG E:GLU14H 3.8 81.9 1.0
CA E:GLU14E 3.9 74.4 1.0
OE1 E:GLU14E 3.9 74.2 1.0
CB D:GLU217 4.2 78.0 1.0
OE2 E:GLU14E 4.3 90.8 1.0
CB E:GLU14H 4.6 73.5 1.0
N E:GLU14E 4.7 75.7 1.0
O E:HOH501 4.8 48.5 1.0
CG D:LYS224 4.8 71.7 1.0
O E:GLU14E 5.0 74.0 1.0
C E:GLU14E 5.0 71.5 1.0
CE D:LYS224 5.0 79.7 1.0

Zinc binding site 5 out of 7 in 6p9u

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Zinc binding site 5 out of 7 in the Crystal Structure of Human Thrombin Mutant W215A


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 Human Thrombin Mutant W215A within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn401

b:70.2
occ:1.00
 OD2 E:ASP1A 1.9 52.4 1.0
NE2 F:HIS119 2.0 83.5 1.0
CE1 F:HIS119 2.9 79.4 1.0
CG E:ASP1A 3.0 54.2 1.0
CD2 F:HIS119 3.0 76.8 1.0
OD1 E:ASP1A 3.4 46.6 1.0
NZ E:LYS9 3.7 51.8 1.0
ND1 F:HIS119 4.0 77.5 1.0
CG F:HIS119 4.1 73.2 1.0
CB E:ASP1A 4.3 59.5 1.0
CG E:PRO5 4.7 53.8 1.0
O E:ASP1A 4.8 71.0 1.0

Zinc binding site 6 out of 7 in 6p9u

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Zinc binding site 6 out of 7 in the Crystal Structure of Human Thrombin Mutant W215A


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 Human Thrombin Mutant W215A within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn301

b:66.0
occ:0.50
 CD F:GLU217 1.7 77.6 1.0
OE1 F:GLU217 2.0 76.7 1.0
OE1 A:GLU14H 2.0 72.8 1.0
OE2 F:GLU217 2.0 73.7 1.0
CG F:GLU217 2.6 74.8 1.0
CD A:GLU14H 2.7 75.2 1.0
OE2 A:GLU14H 2.8 75.2 1.0
CG A:GLU14E 3.2 83.5 1.0
CB F:GLU217 3.5 78.9 1.0
CA A:GLU14E 3.9 77.3 1.0
CG A:GLU14H 4.0 71.8 1.0
CB A:GLU14E 4.0 81.9 1.0
OE1 A:GLU14E 4.1 93.7 1.0
CD A:GLU14E 4.1 91.8 1.0
CB A:GLU14H 4.4 68.3 1.0
O A:GLU14E 4.6 69.8 1.0
N A:GLU14E 4.8 73.0 1.0
C A:GLU14E 4.8 71.6 1.0
O F:HOH801 4.8 41.7 1.0
CA F:GLU217 4.9 76.5 1.0

Zinc binding site 7 out of 7 in 6p9u

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Zinc binding site 7 out of 7 in the Crystal Structure of Human Thrombin Mutant W215A


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 Human Thrombin Mutant W215A within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn401

b:66.0
occ:1.00
 OD2 G:ASP1A 2.0 69.2 1.0
NE2 H:HIS119 2.3 69.4 1.0
CE1 H:HIS119 3.1 73.0 1.0
CG G:ASP1A 3.2 69.0 1.0
NZ G:LYS9 3.3 65.5 1.0
CD2 H:HIS119 3.4 66.3 1.0
CB G:ASP1A 3.9 65.2 1.0
OD1 G:ASP1A 4.2 69.3 1.0
ND1 H:HIS119 4.3 72.7 1.0
CG H:HIS119 4.5 69.5 1.0
CE G:LYS9 4.6 61.8 1.0
O G:ASP1A 4.8 60.7 1.0

Reference:

L.A.Pelc, S.K.Koester, Z.Chen, N.E.Gistover, E.Di Cera. Residues W215, E217 and E192 Control the Allosteric E*-E Equilibrium of Thrombin. Sci Rep V. 9 12304 2019.
ISSN: ESSN 2045-2322
PubMed: 31444378
DOI: 10.1038/S41598-019-48839-1
Page generated: Wed Dec 16 12:29:20 2020

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