Chlorine in PDB 6zlf: Aerobic Crystal Structure of F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution Under 125 Bars of Krypton

Protein crystallography data

The structure of Aerobic Crystal Structure of F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution Under 125 Bars of Krypton, PDB code: 6zlf was solved by S.Engilberge, T.Wagner, P.Carpentier, E.Girard, S.Shima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.40 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 75.025, 162.553, 134.376, 90.00, 93.75, 90.00
R / Rfree (%) 18.2 / 19.7

Other elements in 6zlf:

The structure of Aerobic Crystal Structure of F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution Under 125 Bars of Krypton also contains other interesting chemical elements:

Krypton (Kr) 48 atoms
Iron (Fe) 16 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Aerobic Crystal Structure of F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution Under 125 Bars of Krypton (pdb code 6zlf). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Aerobic Crystal Structure of F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution Under 125 Bars of Krypton, PDB code: 6zlf:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 6zlf

Go back to Chlorine Binding Sites List in 6zlf
Chlorine binding site 1 out of 8 in the Aerobic Crystal Structure of F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution Under 125 Bars of Krypton


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Aerobic Crystal Structure of F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution Under 125 Bars of Krypton within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl514

b:41.9
occ:1.00
 OG A:SER121 3.0 42.8 1.0
N A:SER121 3.3 47.4 1.0
CB A:SER121 3.4 43.9 1.0
CA A:PHE119 3.5 43.1 1.0
C A:PHE119 3.5 44.9 1.0
N A:PRO120 3.6 47.5 1.0
CB A:PHE119 3.6 43.3 1.0
CD A:PRO120 3.8 49.8 1.0
CA A:SER121 3.9 47.9 1.0
O A:PHE119 4.1 42.7 1.0
CG A:PRO94 4.2 41.0 1.0
CB A:PRO94 4.2 37.6 1.0
C A:PRO120 4.3 48.4 1.0
CA A:PRO120 4.4 47.0 1.0
CD1 A:PHE119 4.6 42.6 1.0
CG A:PHE119 4.6 42.6 1.0
O A:HOH700 4.7 49.4 1.0
C A:SER121 4.9 46.6 1.0
N A:LEU122 4.9 41.8 1.0
N A:PHE119 4.9 40.1 1.0
CG A:PRO120 4.9 54.7 1.0
CB A:PRO120 4.9 49.1 1.0

Chlorine binding site 2 out of 8 in 6zlf

Go back to Chlorine Binding Sites List in 6zlf
Chlorine binding site 2 out of 8 in the Aerobic Crystal Structure of F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution Under 125 Bars of Krypton


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Aerobic Crystal Structure of F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution Under 125 Bars of Krypton within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl507

b:41.1
occ:1.00
 OG F:SER121 3.0 41.4 1.0
O F:HOH844 3.1 54.4 1.0
O F:HOH865 3.2 49.9 1.0
N F:SER121 3.4 38.2 1.0
CB F:SER121 3.5 46.0 1.0
CA F:PHE119 3.6 37.6 1.0
CB F:PHE119 3.6 37.5 1.0
C F:PHE119 3.6 38.1 1.0
N F:PRO120 3.7 41.8 1.0
CD F:PRO120 3.9 44.7 1.0
CA F:SER121 4.0 42.6 1.0
CG F:PRO94 4.1 38.1 1.0
CB F:PRO94 4.2 34.9 1.0
O F:PHE119 4.2 35.0 1.0
C F:PRO120 4.4 41.5 1.0
CD1 F:PHE119 4.5 37.1 1.0
CG F:PHE119 4.6 37.6 1.0
CA F:PRO120 4.6 41.5 1.0
O F:HOH611 4.8 48.6 1.0
N F:PHE119 5.0 38.9 1.0
C F:SER121 5.0 41.9 1.0

Chlorine binding site 3 out of 8 in 6zlf

Go back to Chlorine Binding Sites List in 6zlf
Chlorine binding site 3 out of 8 in the Aerobic Crystal Structure of F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution Under 125 Bars of Krypton


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Aerobic Crystal Structure of F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution Under 125 Bars of Krypton within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl510

b:38.9
occ:1.00
 OG G:SER121 3.1 40.5 1.0
N G:SER121 3.4 36.6 1.0
CB G:SER121 3.5 43.3 1.0
CA G:PHE119 3.5 31.7 1.0
C G:PHE119 3.6 35.5 1.0
N G:PRO120 3.6 37.2 1.0
CB G:PHE119 3.6 32.7 1.0
O G:HOH860 3.7 60.9 1.0
CD G:PRO120 3.8 36.2 1.0
CA G:SER121 4.0 37.2 1.0
O G:PHE119 4.2 35.1 1.0
CG G:PRO94 4.2 35.0 1.0
CB G:PRO94 4.2 30.8 1.0
C G:PRO120 4.4 38.5 1.0
CA G:PRO120 4.5 38.9 1.0
CD1 G:PHE119 4.5 34.5 1.0
CG G:PHE119 4.6 33.7 1.0
O G:HOH609 4.8 42.2 1.0
CG G:PRO120 4.9 38.4 1.0
N G:PHE119 4.9 33.7 1.0
CB G:PRO120 4.9 41.0 1.0
C G:SER121 5.0 38.8 1.0

Chlorine binding site 4 out of 8 in 6zlf

Go back to Chlorine Binding Sites List in 6zlf
Chlorine binding site 4 out of 8 in the Aerobic Crystal Structure of F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution Under 125 Bars of Krypton


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Aerobic Crystal Structure of F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution Under 125 Bars of Krypton within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl710

b:45.6
occ:1.00
 OG H:SER121 3.1 48.2 1.0
N H:SER121 3.5 51.8 1.0
CB H:SER121 3.5 51.4 1.0
CA H:PHE119 3.6 47.1 1.0
C H:PHE119 3.6 47.8 1.0
CB H:PHE119 3.7 45.2 1.0
N H:PRO120 3.7 52.4 1.0
CD H:PRO120 3.8 52.8 1.0
CA H:SER121 4.1 50.1 1.0
CG H:PRO94 4.2 43.0 1.0
CB H:PRO94 4.2 43.0 1.0
O H:PHE119 4.3 45.0 1.0
C H:PRO120 4.5 53.5 1.0
CD1 H:PHE119 4.5 43.4 1.0
CA H:PRO120 4.6 53.3 1.0
CG H:PHE119 4.6 43.9 1.0
N H:PHE119 5.0 43.2 1.0
CG H:PRO120 5.0 50.8 1.0

Chlorine binding site 5 out of 8 in 6zlf

Go back to Chlorine Binding Sites List in 6zlf
Chlorine binding site 5 out of 8 in the Aerobic Crystal Structure of F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution Under 125 Bars of Krypton


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Aerobic Crystal Structure of F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution Under 125 Bars of Krypton within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Cl516

b:38.5
occ:1.00
 O I:HOH867 3.0 49.0 1.0
OG I:SER121 3.0 35.1 1.0
N I:SER121 3.4 34.8 1.0
CB I:SER121 3.5 36.2 1.0
O I:HOH895 3.5 57.3 1.0
CA I:PHE119 3.6 30.7 1.0
C I:PHE119 3.7 34.7 1.0
CB I:PHE119 3.7 31.6 1.0
N I:PRO120 3.7 36.5 1.0
CD I:PRO120 3.9 38.3 1.0
CA I:SER121 4.0 34.1 1.0
CG I:PRO94 4.1 28.3 1.0
CB I:PRO94 4.1 32.7 1.0
O I:PHE119 4.3 34.5 1.0
C I:PRO120 4.5 38.5 1.0
CD1 I:PHE119 4.5 31.9 1.0
CA I:PRO120 4.6 36.9 1.0
CG I:PHE119 4.6 31.8 1.0
O I:HOH611 4.8 42.0 1.0
C I:SER121 5.0 35.5 1.0

Chlorine binding site 6 out of 8 in 6zlf

Go back to Chlorine Binding Sites List in 6zlf
Chlorine binding site 6 out of 8 in the Aerobic Crystal Structure of F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution Under 125 Bars of Krypton


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Aerobic Crystal Structure of F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution Under 125 Bars of Krypton within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Cl512

b:38.1
occ:1.00
 OG J:SER121 3.1 39.1 1.0
O J:HOH855 3.1 38.7 1.0
N J:SER121 3.4 37.7 1.0
CA J:PHE119 3.5 32.2 1.0
CB J:SER121 3.5 41.5 1.0
C J:PHE119 3.6 35.5 1.0
N J:PRO120 3.6 36.5 1.0
CB J:PHE119 3.6 29.7 1.0
CD J:PRO120 3.7 35.5 1.0
CA J:SER121 4.0 35.1 1.0
CG J:PRO94 4.2 34.2 1.0
O J:PHE119 4.2 33.6 1.0
CB J:PRO94 4.2 32.5 1.0
C J:PRO120 4.4 38.5 1.0
CA J:PRO120 4.5 40.5 1.0
CD1 J:PHE119 4.5 31.2 1.0
CG J:PHE119 4.6 31.4 1.0
CG J:PRO120 4.9 40.5 1.0
N J:PHE119 4.9 32.3 1.0
CB J:PRO120 4.9 41.8 1.0
O J:HOH628 4.9 39.9 1.0
C J:SER121 5.0 38.2 1.0

Chlorine binding site 7 out of 8 in 6zlf

Go back to Chlorine Binding Sites List in 6zlf
Chlorine binding site 7 out of 8 in the Aerobic Crystal Structure of F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution Under 125 Bars of Krypton


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Aerobic Crystal Structure of F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution Under 125 Bars of Krypton within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Cl512

b:43.6
occ:1.00
 OG K:SER121 3.0 62.8 1.0
O K:HOH829 3.1 57.9 1.0
N K:SER121 3.4 46.5 1.0
O K:HOH812 3.4 63.4 1.0
CB K:SER121 3.5 46.5 1.0
CA K:PHE119 3.6 43.0 1.0
C K:PHE119 3.6 43.4 1.0
CB K:PHE119 3.7 45.1 1.0
N K:PRO120 3.7 47.3 1.0
CD K:PRO120 3.8 45.2 1.0
CA K:SER121 4.0 44.2 1.0
CG K:PRO94 4.2 39.6 1.0
CB K:PRO94 4.2 36.1 1.0
O K:PHE119 4.2 41.2 1.0
C K:PRO120 4.4 51.2 1.0
CD1 K:PHE119 4.5 42.0 1.0
CA K:PRO120 4.5 50.2 1.0
CG K:PHE119 4.6 42.8 1.0
O K:HOH630 4.8 47.8 1.0
CG K:PRO120 5.0 48.6 1.0
N K:PHE119 5.0 39.7 1.0
C K:SER121 5.0 46.0 1.0
CB K:PRO120 5.0 51.1 1.0

Chlorine binding site 8 out of 8 in 6zlf

Go back to Chlorine Binding Sites List in 6zlf
Chlorine binding site 8 out of 8 in the Aerobic Crystal Structure of F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution Under 125 Bars of Krypton


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Aerobic Crystal Structure of F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution Under 125 Bars of Krypton within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Cl510

b:35.2
occ:1.00
 O L:HOH867 2.9 60.8 1.0
OG L:SER121 3.0 38.9 1.0
O L:HOH869 3.3 51.5 1.0
N L:SER121 3.4 36.3 1.0
CB L:SER121 3.5 41.9 1.0
CA L:PHE119 3.5 30.5 1.0
C L:PHE119 3.6 33.9 1.0
N L:PRO120 3.6 37.5 1.0
CB L:PHE119 3.6 32.9 1.0
CD L:PRO120 3.8 40.9 1.0
CA L:SER121 4.0 34.3 1.0
CG L:PRO94 4.1 33.5 1.0
CB L:PRO94 4.2 33.4 1.0
O L:PHE119 4.2 31.8 1.0
C L:PRO120 4.4 39.0 1.0
CD1 L:PHE119 4.5 35.2 1.0
CA L:PRO120 4.5 36.6 1.0
CG L:PHE119 4.6 33.7 1.0
CG L:PRO120 4.7 46.6 1.0
O L:HOH693 4.8 42.8 1.0
N L:PHE119 4.9 33.0 1.0
C L:SER121 4.9 36.9 1.0

Reference:

S.Engilberge, T.Wagner, P.Carpentier, E.Girard, S.Shima. Krypton-Derivatization Highlights O 2 -Channeling in A Four-Electron Reducing Oxidase. Chem.Commun.(Camb.) V. 56 10863 2020.
ISSN: ESSN 1364-548X
PubMed: 32940290
DOI: 10.1039/D0CC04557H
Page generated: Sat Dec 12 14:47:17 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy