Zinc in PDB 6vjv: Crystal Structure of the Prochlorococcus Phage (Myovirus P-SSM2) Ferredoxin at 1.6 Angstroms

Protein crystallography data

The structure of Crystal Structure of the Prochlorococcus Phage (Myovirus P-SSM2) Ferredoxin at 1.6 Angstroms, PDB code: 6vjv was solved by J.L.Olmos Jr., I.J.Campbell, M.D.Miller, W.Xu, D.Kahanda, J.T.Atkinson, N.Sparks, G.N.Bennett, J.J.Silberg, G.N.Phillips Jr., with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.06 / 1.59
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 52.619, 31.446, 61.288, 90.00, 92.48, 90.00
R / Rfree (%) 17.8 / 21.3

Other elements in 6vjv:

The structure of Crystal Structure of the Prochlorococcus Phage (Myovirus P-SSM2) Ferredoxin at 1.6 Angstroms also contains other interesting chemical elements:

Iron (Fe) 4 atoms

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of the Prochlorococcus Phage (Myovirus P-SSM2) Ferredoxin at 1.6 Angstroms (pdb code 6vjv). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 15 binding sites of Zinc where determined in the Crystal Structure of the Prochlorococcus Phage (Myovirus P-SSM2) Ferredoxin at 1.6 Angstroms, PDB code: 6vjv:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 15 in 6vjv

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Zinc binding site 1 out of 15 in the Crystal Structure of the Prochlorococcus Phage (Myovirus P-SSM2) Ferredoxin at 1.6 Angstroms


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 the Prochlorococcus Phage (Myovirus P-SSM2) Ferredoxin at 1.6 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn104

b:37.5
occ:0.37
ZN A:ZN104 0.0 37.5 0.4
O A:HOH205 1.7 47.6 1.0
O A:HOH226 2.0 49.7 1.0
OE2 A:GLU72 2.0 37.0 1.0
OD2 A:ASP97 2.3 43.3 0.5
OE1 A:GLU72 2.3 34.4 1.0
CD A:GLU72 2.5 34.8 1.0
ZN A:ZN104 2.5 59.9 0.6
CG A:ASP97 3.1 25.0 0.5
OD1 A:ASP97 3.2 32.0 0.5
O A:HOH261 3.5 20.5 0.5
HB2 A:ASP97 3.6 32.6 0.5
HZ3 A:LYS51 3.7 38.1 1.0
HZ2 A:TRP74 3.9 28.1 1.0
HE1 A:TRP74 3.9 28.6 1.0
CG A:GLU72 4.0 29.3 1.0
HB3 A:ASP97 4.1 32.6 0.5
HZ1 A:LYS51 4.2 38.1 1.0
HG3 A:GLU72 4.2 35.2 1.0
CB A:ASP97 4.3 27.2 0.5
O A:HOH291 4.3 60.3 1.0
HG2 A:GLU72 4.3 35.2 1.0
OD2 A:ASP97 4.3 35.7 0.5
NZ A:LYS51 4.4 31.7 1.0
CB A:ASP97 4.5 28.3 0.5
O A:HOH215 4.5 36.4 1.0
NE1 A:TRP74 4.5 23.9 1.0
CZ2 A:TRP74 4.6 23.4 1.0
HB3 A:ASP97 4.7 34.0 0.5
CG A:ASP97 4.8 31.4 0.5
HB2 A:ASP97 4.8 34.0 0.5
O A:HOH252 4.9 29.9 1.0
HZ2 A:LYS51 4.9 38.1 1.0
CE2 A:TRP74 4.9 21.2 1.0

Zinc binding site 2 out of 15 in 6vjv

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Zinc binding site 2 out of 15 in the Crystal Structure of the Prochlorococcus Phage (Myovirus P-SSM2) Ferredoxin at 1.6 Angstroms


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 the Prochlorococcus Phage (Myovirus P-SSM2) Ferredoxin at 1.6 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn104

b:59.9
occ:0.63
ZN A:ZN104 0.0 59.9 0.6
OD2 A:ASP97 1.5 43.3 0.5
O A:HOH291 2.1 60.3 1.0
O A:HOH226 2.3 49.7 1.0
OD2 A:ASP97 2.5 35.7 0.5
ZN A:ZN104 2.5 37.5 0.4
O A:HOH205 2.5 47.6 1.0
CG A:ASP97 2.7 25.0 0.5
HB3 A:ASP97 3.1 32.6 0.5
HB2 A:ASP97 3.2 32.6 0.5
CG A:ASP97 3.3 31.4 0.5
HB2 A:ASP97 3.3 34.0 0.5
CB A:ASP97 3.4 27.2 0.5
CB A:ASP97 3.4 28.3 0.5
HB3 A:ASP97 3.5 34.0 0.5
OD1 A:ASP97 3.7 32.0 0.5
O A:HOH228 4.2 25.1 1.0
O A:HOH204 4.2 41.1 1.0
OE1 A:GLU72 4.4 34.4 1.0
O A:HOH261 4.5 20.5 0.5
OD1 A:ASP97 4.5 38.2 0.5
OE2 A:GLU72 4.5 37.0 1.0
O A:HOH215 4.6 36.4 1.0
CA A:ASP97 4.9 30.3 0.5
CD A:GLU72 4.9 34.8 1.0
CA A:ASP97 4.9 29.4 0.5

Zinc binding site 3 out of 15 in 6vjv

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Zinc binding site 3 out of 15 in the Crystal Structure of the Prochlorococcus Phage (Myovirus P-SSM2) Ferredoxin at 1.6 Angstroms


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 the Prochlorococcus Phage (Myovirus P-SSM2) Ferredoxin at 1.6 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn105

b:53.7
occ:1.00
OE1 A:GLU54 2.2 50.2 1.0
O A:HOH213 2.4 51.6 1.0
CD A:GLU54 3.1 43.0 1.0
OE2 A:GLU54 3.4 44.8 1.0
O A:HOH331 3.8 51.2 1.0
O A:HOH317 4.3 34.2 1.0
HB3 A:GLU54 4.5 30.8 1.0
CG A:GLU54 4.5 32.6 1.0
HG23 A:VAL87 4.7 22.9 1.0
HG21 A:VAL87 4.8 22.9 1.0
HB2 A:GLU54 4.9 30.8 1.0
HG2 A:GLU54 4.9 39.1 1.0
CB A:GLU54 4.9 25.6 1.0

Zinc binding site 4 out of 15 in 6vjv

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Zinc binding site 4 out of 15 in the Crystal Structure of the Prochlorococcus Phage (Myovirus P-SSM2) Ferredoxin at 1.6 Angstroms


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 the Prochlorococcus Phage (Myovirus P-SSM2) Ferredoxin at 1.6 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn106

b:28.5
occ:1.00
OXT B:ACT102 1.1 25.9 1.0
C B:ACT102 1.8 39.1 1.0
OE1 A:GLU14 2.1 22.1 1.0
OE1 B:GLU14 2.2 26.4 1.0
O B:ACT102 2.2 44.7 1.0
O A:HOH299 2.3 31.6 1.0
OE2 A:GLU14 2.3 22.9 1.0
OE2 B:GLU14 2.4 22.4 1.0
CD A:GLU14 2.5 19.8 1.0
CD B:GLU14 2.6 22.7 1.0
HH21 B:ARG8 3.2 28.4 1.0
CH3 B:ACT102 3.3 36.4 1.0
HH21 A:ARG8 3.5 29.9 1.0
H1 B:ACT102 3.6 43.7 1.0
H3 B:ACT102 3.6 43.7 1.0
O A:HOH207 3.9 45.2 1.0
H2 B:ACT102 3.9 43.7 1.0
NH2 B:ARG8 3.9 23.6 1.0
CG A:GLU14 4.0 19.9 1.0
HE B:ARG8 4.0 25.5 1.0
HE A:ARG8 4.0 27.7 1.0
CG B:GLU14 4.1 19.6 1.0
O B:HOH210 4.1 36.7 1.0
O B:HOH211 4.2 53.6 1.0
NH2 A:ARG8 4.3 24.9 1.0
O B:HOH222 4.3 39.8 1.0
HH22 B:ARG8 4.3 28.4 1.0
HG2 A:GLU14 4.4 23.8 1.0
HG3 A:GLU14 4.5 23.8 1.0
HG21 B:THR6 4.5 20.6 1.0
HG2 B:GLU14 4.5 23.5 1.0
HB3 A:GLU14 4.5 22.4 1.0
HG3 B:GLU14 4.6 23.5 1.0
HG21 A:THR6 4.6 25.6 1.0
HG23 B:THR6 4.6 20.6 1.0
NE B:ARG8 4.6 21.2 1.0
HB2 A:GLU14 4.7 22.4 1.0
NE A:ARG8 4.7 23.1 1.0
CB A:GLU14 4.7 18.6 1.0
HH22 A:ARG8 4.7 29.9 1.0
CZ B:ARG8 4.7 18.7 1.0
HB3 B:GLU14 4.7 22.3 1.0
HG23 A:THR6 4.8 25.6 1.0
CB B:GLU14 4.9 18.6 1.0
CZ A:ARG8 4.9 19.6 1.0
HB2 B:GLU14 4.9 22.3 1.0

Zinc binding site 5 out of 15 in 6vjv

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Zinc binding site 5 out of 15 in the Crystal Structure of the Prochlorococcus Phage (Myovirus P-SSM2) Ferredoxin at 1.6 Angstroms


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 the Prochlorococcus Phage (Myovirus P-SSM2) Ferredoxin at 1.6 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn107

b:22.2
occ:1.00
O A:ACT102 1.9 23.6 1.0
OD2 A:ASP66 1.9 25.5 1.0
OD2 A:ASP68 2.2 36.1 1.0
OD1 A:ASP68 2.2 34.6 1.0
CG A:ASP68 2.5 29.3 1.0
CG A:ASP66 2.7 21.8 1.0
OD1 A:ASP66 2.9 20.5 1.0
C A:ACT102 3.0 14.5 1.0
H1 A:ACT102 3.3 28.2 1.0
H3 A:ACT102 3.3 28.2 1.0
CH3 A:ACT102 3.4 23.6 1.0
HG3 A:GLN69 3.8 23.5 1.0
O A:HOH232 4.0 28.4 1.0
CB A:ASP68 4.0 29.3 1.0
H A:ASP68 4.1 29.8 1.0
OXT A:ACT102 4.2 23.0 1.0
CB A:ASP66 4.2 24.1 1.0
H A:GLN69 4.3 25.1 1.0
H2 A:ACT102 4.4 28.2 1.0
HB2 A:ASP66 4.4 28.9 1.0
O A:HOH312 4.4 55.4 1.0
HB3 A:ASP68 4.4 35.1 1.0
HB2 A:ASP68 4.4 35.1 1.0
HB3 A:ASP66 4.5 28.9 1.0
CG A:GLN69 4.7 19.6 1.0
N A:ASP68 4.8 24.8 1.0
N A:GLN69 4.8 20.9 1.0
CA A:ASP68 4.8 25.5 1.0

Zinc binding site 6 out of 15 in 6vjv

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Zinc binding site 6 out of 15 in the Crystal Structure of the Prochlorococcus Phage (Myovirus P-SSM2) Ferredoxin at 1.6 Angstroms


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 the Prochlorococcus Phage (Myovirus P-SSM2) Ferredoxin at 1.6 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn108

b:21.1
occ:1.00
OD2 A:ASP31 1.9 20.6 1.0
OE2 A:GLU27 1.9 20.3 1.0
O A:HOH297 2.0 22.1 1.0
CD A:GLU27 2.7 21.5 1.0
CG A:ASP31 2.8 22.2 1.0
OE1 A:GLU27 2.8 23.9 1.0
OD1 A:ASP31 2.9 18.3 1.0
HE21 A:GLN23 3.6 19.5 1.0
O A:HOH262 3.8 46.4 1.0
O A:HOH275 4.0 18.2 1.0
HE22 A:GLN23 4.1 19.5 1.0
NE2 A:GLN23 4.1 16.2 1.0
CG A:GLU27 4.1 17.1 1.0
CB A:ASP31 4.2 17.2 1.0
HG2 A:GLU27 4.3 20.5 1.0
HB2 A:ASP31 4.4 20.6 1.0
HB3 A:ASP31 4.4 20.6 1.0
HG3 A:GLU27 4.5 20.5 1.0
O A:HOH253 4.7 29.0 1.0
O A:GLU27 4.7 14.3 1.0
HA A:ALA28 4.8 17.1 1.0

Zinc binding site 7 out of 15 in 6vjv

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Zinc binding site 7 out of 15 in the Crystal Structure of the Prochlorococcus Phage (Myovirus P-SSM2) Ferredoxin at 1.6 Angstroms


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 the Prochlorococcus Phage (Myovirus P-SSM2) Ferredoxin at 1.6 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn109

b:21.8
occ:1.00
O A:HOH290 1.9 24.8 1.0
OE2 A:GLU93 2.0 24.9 1.0
OE1 A:GLU93 2.6 22.3 1.0
CD A:GLU93 2.6 22.5 1.0
O A:HOH243 4.1 40.9 1.0
CG A:GLU93 4.1 20.4 1.0
HG2 A:GLU93 4.3 24.4 1.0
HG3 A:GLU93 4.5 24.4 1.0
HA A:ALA47 4.5 21.1 1.0
HB2 A:ALA47 4.7 22.8 1.0
HB3 A:GLU93 5.0 21.4 1.0

Zinc binding site 8 out of 15 in 6vjv

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Zinc binding site 8 out of 15 in the Crystal Structure of the Prochlorococcus Phage (Myovirus P-SSM2) Ferredoxin at 1.6 Angstroms


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of the Prochlorococcus Phage (Myovirus P-SSM2) Ferredoxin at 1.6 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn110

b:26.5
occ:0.49
OXT A:ACT103 1.4 32.5 1.0
C A:ACT103 1.5 27.1 1.0
O A:ACT103 1.6 52.2 1.0
OE2 A:GLU20 2.1 30.6 1.0
N A:ALA2 2.2 28.6 1.0
O A:HOH206 2.3 40.6 0.7
OE1 A:GLU20 2.3 23.9 1.0
O A:HOH217 2.5 49.7 1.0
O A:HOH203 2.6 52.5 1.0
CD A:GLU20 2.6 22.9 1.0
HA A:ALA2 2.9 35.4 1.0
O A:HOH206 3.0 44.5 0.3
CA A:ALA2 3.0 29.5 1.0
CH3 A:ACT103 3.2 33.2 1.0
HB2 A:ALA2 3.3 39.4 1.0
H1 A:ACT103 3.6 39.9 1.0
H2 A:ACT103 3.6 39.9 1.0
H3 A:ACT103 3.6 39.9 1.0
CB A:ALA2 3.7 32.8 1.0
O A:HOH307 4.0 48.4 1.0
CG A:GLU20 4.1 19.9 1.0
HB3 A:ALA2 4.2 39.4 1.0
HA A:GLU20 4.3 22.4 1.0
C A:ALA2 4.4 22.7 1.0
HG2 A:GLU20 4.5 23.9 1.0
HB1 A:ALA2 4.5 39.4 1.0
HG3 A:GLU20 4.6 23.9 1.0
H A:GLU21 4.6 25.0 0.4
H A:GLU21 4.7 25.0 0.6
HB3 A:GLU20 4.9 22.7 1.0
O A:ALA2 4.9 23.9 1.0
CB A:GLU20 5.0 18.9 1.0

Zinc binding site 9 out of 15 in 6vjv

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Zinc binding site 9 out of 15 in the Crystal Structure of the Prochlorococcus Phage (Myovirus P-SSM2) Ferredoxin at 1.6 Angstroms


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of the Prochlorococcus Phage (Myovirus P-SSM2) Ferredoxin at 1.6 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn104

b:79.2
occ:1.00
O B:HOH223 1.8 69.2 1.0
O B:HOH244 2.1 66.0 1.0
O B:HOH204 3.2 67.8 1.0
OD2 B:ASP22 3.3 31.9 1.0
OD1 B:ASP22 3.6 28.6 1.0
CG B:ASP22 3.8 29.9 1.0
O B:HOH258 4.4 37.1 1.0
HG3 B:GLU20 4.4 30.9 1.0
HB3 B:GLU20 4.8 28.1 1.0
O B:HOH255 4.9 65.9 1.0

Zinc binding site 10 out of 15 in 6vjv

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Zinc binding site 10 out of 15 in the Crystal Structure of the Prochlorococcus Phage (Myovirus P-SSM2) Ferredoxin at 1.6 Angstroms


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of the Prochlorococcus Phage (Myovirus P-SSM2) Ferredoxin at 1.6 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn105

b:36.4
occ:0.50
O B:HOH240 2.2 41.0 1.0
OE2 B:GLU20 2.2 44.5 1.0
N B:ALA2 2.3 33.0 1.0
OE1 B:GLU20 2.3 44.0 1.0
HB2 B:ALA2 2.4 47.6 1.0
CD B:GLU20 2.7 36.3 1.0
CA B:ALA2 2.9 37.3 1.0
HA B:ALA2 3.0 44.8 1.0
CB B:ALA2 3.1 39.7 1.0
HB3 B:ALA2 3.7 47.6 1.0
HB1 B:ALA2 3.8 47.6 1.0
CG B:GLU20 4.2 25.7 1.0
C B:ALA2 4.4 34.0 1.0
HA B:GLU20 4.5 27.3 1.0
HG2 B:GLU20 4.5 30.9 1.0
HG3 B:GLU20 4.6 30.9 1.0
O B:ALA2 4.9 31.8 1.0

Reference:

I.J.Campbell, J.L.Olmos Jr., W.Xu, D.Kahanda, J.T.Atkinson, N.Sparks, M.D.Miller, G.N.Phillips Jr., G.N.Bennett, J.J.Silberg. Prochlorococcus Phage Ferredoxin: Structural Characterization and Interactions with Cyanobacterial Sulfite Reductases To Be Published.
Page generated: Wed Dec 16 13:01:58 2020

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