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Zinc in PDB 6bm9: Directed Evolutionary Changes in Mbl Super Family - Vim-2 Round 10

Protein crystallography data

The structure of Directed Evolutionary Changes in Mbl Super Family - Vim-2 Round 10, PDB code: 6bm9 was solved by N.-S.Hong, C.J.Jackson, P.D.Carr, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.89 / 2.19
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 128.596, 41.672, 156.764, 90.00, 99.41, 90.00
R / Rfree (%) 22.1 / 26.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Directed Evolutionary Changes in Mbl Super Family - Vim-2 Round 10 (pdb code 6bm9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Directed Evolutionary Changes in Mbl Super Family - Vim-2 Round 10, PDB code: 6bm9:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6bm9

Go back to Zinc Binding Sites List in 6bm9
Zinc binding site 1 out of 4 in the Directed Evolutionary Changes in Mbl Super Family - Vim-2 Round 10


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Directed Evolutionary Changes in Mbl Super Family - Vim-2 Round 10 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:69.0
occ:1.00
NE2 A:HIS114 2.5 46.9 1.0
SG B:CYS198 2.5 48.3 1.0
O B:HOH406 2.6 37.3 1.0
CE1 A:HIS114 2.8 46.8 1.0
CG A:PRO68 2.9 49.6 1.0
CB A:PRO68 2.9 47.4 1.0
CD2 A:HIS116 3.6 56.4 1.0
CB B:CYS198 3.7 35.5 1.0
CD2 A:HIS114 3.8 45.0 1.0
ND1 A:HIS114 4.1 46.1 1.0
N B:CYS198 4.2 32.6 1.0
NE2 A:HIS116 4.2 60.8 1.0
CA A:PRO68 4.3 48.6 1.0
CD A:PRO68 4.3 52.2 1.0
CA B:CYS198 4.5 32.1 1.0
CG A:HIS114 4.6 41.2 1.0
N A:PRO68 4.7 51.4 1.0
CG A:HIS116 4.8 55.5 1.0
NE2 B:HIS179 4.9 40.0 1.0

Zinc binding site 2 out of 4 in 6bm9

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Zinc binding site 2 out of 4 in the Directed Evolutionary Changes in Mbl Super Family - Vim-2 Round 10


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Directed Evolutionary Changes in Mbl Super Family - Vim-2 Round 10 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:66.9
occ:1.00
CE1 B:HIS116 2.3 64.7 1.0
NE2 B:HIS114 2.3 46.2 1.0
SG A:CYS198 2.5 47.7 1.0
ND1 B:HIS116 2.7 64.0 1.0
CE1 A:HIS179 2.8 44.7 1.0
CD2 B:HIS114 2.9 39.4 1.0
CB A:CYS198 3.0 35.3 1.0
ND1 A:HIS179 3.1 44.9 1.0
NE2 B:HIS116 3.3 69.2 1.0
CE1 B:HIS114 3.4 46.6 1.0
CG B:HIS116 3.8 63.3 1.0
NE2 A:HIS179 3.8 45.7 1.0
CG B:HIS114 4.0 35.6 1.0
CD2 B:HIS116 4.1 68.5 1.0
ND1 B:HIS114 4.2 42.2 1.0
CG A:HIS179 4.3 41.6 1.0
CA A:CYS198 4.5 33.9 1.0
CG B:PRO68 4.5 59.7 1.0
CD2 A:HIS179 4.6 44.3 1.0
N A:CYS198 4.8 25.8 1.0
CB B:HIS116 5.0 54.8 1.0

Zinc binding site 3 out of 4 in 6bm9

Go back to Zinc Binding Sites List in 6bm9
Zinc binding site 3 out of 4 in the Directed Evolutionary Changes in Mbl Super Family - Vim-2 Round 10


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Directed Evolutionary Changes in Mbl Super Family - Vim-2 Round 10 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:72.2
occ:1.00
NE2 C:HIS114 2.1 62.4 1.0
SG D:CYS198 2.4 68.3 1.0
CE1 C:HIS116 2.6 75.7 1.0
ND1 C:HIS116 2.7 73.5 1.0
CE1 C:HIS114 2.8 62.0 1.0
CD2 C:HIS114 3.3 60.1 1.0
CB D:CYS198 3.4 45.3 1.0
NE2 C:HIS116 3.9 75.3 1.0
ND1 C:HIS114 4.0 60.6 1.0
N D:CYS198 4.1 44.7 1.0
CG C:HIS116 4.1 71.6 1.0
CG C:HIS114 4.3 58.2 1.0
CA D:CYS198 4.3 42.2 1.0
CD2 C:HIS116 4.6 73.8 1.0
CE1 D:HIS179 4.7 54.2 1.0

Zinc binding site 4 out of 4 in 6bm9

Go back to Zinc Binding Sites List in 6bm9
Zinc binding site 4 out of 4 in the Directed Evolutionary Changes in Mbl Super Family - Vim-2 Round 10


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Directed Evolutionary Changes in Mbl Super Family - Vim-2 Round 10 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:68.2
occ:1.00
NE2 D:HIS114 2.1 62.6 1.0
CE1 D:HIS116 2.3 54.5 1.0
SG C:CYS198 2.4 53.7 1.0
CD2 D:HIS114 2.8 59.0 1.0
ND1 D:HIS116 2.9 51.5 1.0
CB C:CYS198 2.9 29.8 1.0
CE1 C:HIS179 3.0 50.0 1.0
CE1 D:HIS114 3.1 59.5 1.0
ND1 C:HIS179 3.4 47.8 1.0
NE2 D:HIS116 3.5 62.7 1.0
CG D:HIS114 3.9 52.8 1.0
NE2 C:HIS179 3.9 49.2 1.0
ND1 D:HIS114 4.0 54.7 1.0
CG D:HIS116 4.2 54.6 1.0
CG D:PRO68 4.2 51.4 1.0
CA C:CYS198 4.2 34.2 1.0
N C:CYS198 4.3 34.5 1.0
CG C:HIS179 4.4 44.4 1.0
CD2 D:HIS116 4.5 59.7 1.0
CB D:PRO68 4.6 48.7 1.0
CD2 C:HIS179 4.7 45.9 1.0
ND2 C:ASN210 4.9 76.3 1.0

Reference:

F.Baier, N.Hong, G.Yang, A.Pabis, C.M.Miton, A.Barrozo, P.D.Carr, S.C.Kamerlin, C.J.Jackson, N.Tokuriki. Cryptic Genetic Variation Shapes the Adaptive Evolutionary Potential of Enzymes. Elife V. 8 2019.
ISSN: ESSN 2050-084X
PubMed: 30719972
DOI: 10.7554/ELIFE.40789
Page generated: Wed Dec 16 11:32:30 2020

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