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Iron in PDB 8ad0: X-Ray Structure of Na+-Nqr From Vibrio Cholerae in Different Conformation at 3.1 A

Enzymatic activity of X-Ray Structure of Na+-Nqr From Vibrio Cholerae in Different Conformation at 3.1 A

All present enzymatic activity of X-Ray Structure of Na+-Nqr From Vibrio Cholerae in Different Conformation at 3.1 A:
7.2.1.1;

Protein crystallography data

The structure of X-Ray Structure of Na+-Nqr From Vibrio Cholerae in Different Conformation at 3.1 A, PDB code: 8ad0 was solved by G.Fritz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.12 / 3.11
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 89.31, 142.15, 105.93, 90, 109.83, 90
R / Rfree (%) 24.9 / 28.8

Other elements in 8ad0:

The structure of X-Ray Structure of Na+-Nqr From Vibrio Cholerae in Different Conformation at 3.1 A also contains other interesting chemical elements:

Bromine (Br) 1 atom
Sodium (Na) 1 atom
Potassium (K) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the X-Ray Structure of Na+-Nqr From Vibrio Cholerae in Different Conformation at 3.1 A (pdb code 8ad0). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the X-Ray Structure of Na+-Nqr From Vibrio Cholerae in Different Conformation at 3.1 A, PDB code: 8ad0:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 8ad0

Go back to Iron Binding Sites List in 8ad0
Iron binding site 1 out of 4 in the X-Ray Structure of Na+-Nqr From Vibrio Cholerae in Different Conformation at 3.1 A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of X-Ray Structure of Na+-Nqr From Vibrio Cholerae in Different Conformation at 3.1 A within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe302

b:115.0
occ:1.00
FE1 D:FES302 0.0 115.0 1.0
S1 D:FES302 2.2 117.4 1.0
S2 D:FES302 2.2 118.6 1.0
SG E:CYS26 2.3 107.9 1.0
SG D:CYS112 2.3 121.3 1.0
FE2 D:FES302 2.7 115.6 1.0
HB2 E:CYS26 2.9 127.5 1.0
H D:CYS112 3.0 156.5 1.0
CB E:CYS26 3.2 105.6 1.0
HB2 D:CYS112 3.3 147.7 1.0
H D:GLY27 3.3 155.8 1.0
CB D:CYS112 3.4 122.5 1.0
HB3 E:CYS26 3.7 127.5 1.0
H E:CYS26 3.7 126.0 1.0
N D:CYS112 3.7 129.8 1.0
O D:THR110 3.8 123.3 1.0
N D:GLY27 4.1 129.2 1.0
HA D:LEU26 4.1 141.4 1.0
CA D:CYS112 4.2 129.9 1.0
H D:VAL28 4.2 133.2 1.0
HB3 D:CYS112 4.2 147.7 1.0
HA D:ASN111 4.2 159.5 1.0
H D:CYS29 4.3 129.2 1.0
HA2 D:GLY27 4.3 141.2 1.0
N E:CYS26 4.4 104.3 1.0
O E:VAL118 4.4 122.9 1.0
CA E:CYS26 4.4 104.7 1.0
SG D:CYS29 4.4 106.7 1.0
HG23 E:VAL118 4.5 148.3 1.0
HA E:ASN119 4.5 147.3 1.0
HA D:CYS112 4.6 156.7 1.0
HB2 D:CYS29 4.6 128.6 1.0
CA D:GLY27 4.7 117.0 1.0
SG E:CYS120 4.7 117.1 1.0
C D:ASN111 4.7 133.7 1.0
H E:CYS120 4.8 161.1 1.0
N D:VAL28 4.8 110.4 1.0
HA2 E:GLY24 4.9 145.6 1.0
CA D:ASN111 4.9 132.3 1.0
C D:THR110 5.0 122.4 1.0
HA E:CYS26 5.0 126.4 1.0

Iron binding site 2 out of 4 in 8ad0

Go back to Iron Binding Sites List in 8ad0
Iron binding site 2 out of 4 in the X-Ray Structure of Na+-Nqr From Vibrio Cholerae in Different Conformation at 3.1 A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of X-Ray Structure of Na+-Nqr From Vibrio Cholerae in Different Conformation at 3.1 A within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe302

b:115.6
occ:1.00
FE2 D:FES302 0.0 115.6 1.0
S1 D:FES302 2.2 117.4 1.0
S2 D:FES302 2.2 118.6 1.0
SG E:CYS120 2.3 117.1 1.0
SG D:CYS29 2.3 106.7 1.0
HB2 D:CYS29 2.4 128.6 1.0
FE1 D:FES302 2.7 115.0 1.0
CB D:CYS29 2.8 106.5 1.0
H E:CYS120 3.3 161.1 1.0
H D:CYS29 3.3 129.2 1.0
HB3 D:CYS29 3.4 128.6 1.0
H E:GLY24 3.5 138.0 1.0
HB2 E:CYS120 3.6 158.1 1.0
CB E:CYS120 3.6 131.1 1.0
SG E:CYS26 3.9 107.9 1.0
HA2 E:GLY24 4.0 145.6 1.0
N E:CYS120 4.0 133.6 1.0
N D:CYS29 4.0 107.0 1.0
CA D:CYS29 4.0 106.2 1.0
H E:MET25 4.1 126.9 1.0
O D:THR110 4.1 123.3 1.0
H E:CYS26 4.2 126.0 1.0
N E:GLY24 4.2 114.3 1.0
HB D:THR110 4.3 146.6 1.0
HB3 E:CYS120 4.3 158.1 1.0
HA D:ASN111 4.4 159.5 1.0
HA E:ASN119 4.4 147.3 1.0
CA E:CYS120 4.4 126.8 1.0
O E:VAL118 4.4 122.9 1.0
CA E:GLY24 4.5 120.7 1.0
HA D:CYS29 4.6 128.3 1.0
H D:CYS112 4.7 156.5 1.0
N E:MET25 4.7 105.1 1.0
HG1 D:THR110 4.7 148.9 1.0
HA E:CYS120 4.7 153.0 1.0
H D:SER30 4.8 130.6 1.0
HB2 E:CYS26 4.8 127.5 1.0
SG D:CYS112 4.8 121.3 1.0
HA E:LEU23 4.8 129.4 1.0
C D:THR110 4.9 122.4 1.0
H D:VAL28 4.9 133.2 1.0
HA2 D:GLY27 4.9 141.2 1.0
HB2 E:MET25 5.0 123.7 1.0
C E:GLY24 5.0 107.5 1.0

Iron binding site 3 out of 4 in 8ad0

Go back to Iron Binding Sites List in 8ad0
Iron binding site 3 out of 4 in the X-Ray Structure of Na+-Nqr From Vibrio Cholerae in Different Conformation at 3.1 A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of X-Ray Structure of Na+-Nqr From Vibrio Cholerae in Different Conformation at 3.1 A within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe1502

b:193.9
occ:1.00
FE1 F:FES1502 0.0 193.9 1.0
S1 F:FES1502 2.2 161.3 1.0
S2 F:FES1502 2.2 162.1 1.0
SG F:CYS76 2.3 167.7 1.0
SG F:CYS70 2.4 181.0 1.0
FE2 F:FES1502 2.7 162.2 1.0
H F:CYS76 2.8 195.3 1.0
H F:GLY77 2.9 193.5 1.0
H F:GLY72 3.3 192.7 1.0
H F:CYS70 3.5 209.0 1.0
H F:SER75 3.5 199.7 1.0
N F:CYS76 3.5 162.1 1.0
CB F:CYS76 3.5 167.3 1.0
HB3 F:CYS76 3.6 201.6 1.0
N F:GLY77 3.7 160.6 1.0
CB F:CYS70 3.7 176.0 1.0
HB3 F:CYS70 3.7 212.0 1.0
H F:GLY71 3.7 204.8 1.0
HA F:SER68 3.9 195.5 1.0
CA F:CYS76 3.9 162.4 1.0
H F:GLN78 4.0 216.9 1.0
H F:GLY74 4.1 202.6 1.0
N F:CYS70 4.1 173.5 1.0
N F:GLY72 4.1 159.9 1.0
N F:SER75 4.2 165.7 1.0
SG F:CYS111 4.3 149.0 1.0
HB3 F:CYS79 4.3 192.4 1.0
HA2 F:GLY72 4.3 192.8 1.0
HB2 F:CYS76 4.3 201.6 1.0
N F:GLY71 4.3 170.0 1.0
C F:CYS76 4.3 163.2 1.0
H F:CYS79 4.3 193.6 1.0
CA F:CYS70 4.4 171.8 1.0
HA2 F:GLY74 4.4 203.2 1.0
HB2 F:CYS70 4.4 212.0 1.0
HA2 F:GLY77 4.5 193.1 1.0
SG F:CYS79 4.5 195.6 1.0
C F:SER75 4.6 160.2 1.0
CA F:GLY72 4.6 160.0 1.0
CA F:GLY77 4.6 160.3 1.0
O F:GLY72 4.6 168.8 1.0
HB3 F:SER75 4.6 191.4 1.0
N F:GLN78 4.6 180.1 1.0
C F:GLY72 4.6 167.7 1.0
N F:GLY74 4.7 168.1 1.0
C F:CYS70 4.7 168.5 1.0
CA F:SER68 4.7 162.2 1.0
HA F:CYS76 4.8 195.7 1.0
CA F:GLY74 4.9 168.6 1.0
C F:SER68 4.9 167.3 1.0
CA F:SER75 4.9 161.4 1.0
CB F:CYS79 4.9 159.7 1.0
HB2 F:SER68 4.9 190.6 1.0
HB3 F:CYS111 4.9 173.7 1.0
H F:ALA69 5.0 207.5 1.0
N F:CYS79 5.0 160.7 1.0

Iron binding site 4 out of 4 in 8ad0

Go back to Iron Binding Sites List in 8ad0
Iron binding site 4 out of 4 in the X-Ray Structure of Na+-Nqr From Vibrio Cholerae in Different Conformation at 3.1 A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of X-Ray Structure of Na+-Nqr From Vibrio Cholerae in Different Conformation at 3.1 A within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe1502

b:162.2
occ:1.00
FE2 F:FES1502 0.0 162.2 1.0
SG F:CYS111 2.2 149.0 1.0
S2 F:FES1502 2.2 162.1 1.0
S1 F:FES1502 2.2 161.3 1.0
SG F:CYS79 2.3 195.6 1.0
FE1 F:FES1502 2.7 193.9 1.0
HB3 F:CYS111 2.9 173.7 1.0
CB F:CYS111 3.2 144.1 1.0
HB3 F:CYS79 3.3 192.4 1.0
CB F:CYS79 3.5 159.7 1.0
H F:CYS111 3.5 172.3 1.0
HA2 F:GLY72 3.6 192.8 1.0
HB3 F:LEU109 3.7 166.7 1.0
HB2 F:CYS111 3.8 173.7 1.0
H F:GLY74 3.8 202.6 1.0
HD12 F:LEU56 3.9 196.1 1.0
H F:CYS79 3.9 193.6 1.0
H F:GLY72 3.9 192.7 1.0
HA2 F:GLY74 4.0 203.2 1.0
HB2 F:CYS79 4.1 192.4 1.0
H F:GLY77 4.1 193.5 1.0
N F:CYS111 4.2 142.9 1.0
CA F:CYS111 4.3 141.5 1.0
HD13 F:LEU109 4.3 171.0 1.0
HD13 F:LEU56 4.4 196.1 1.0
CA F:GLY72 4.4 160.0 1.0
SG F:CYS76 4.4 167.7 1.0
SG F:CYS70 4.5 181.0 1.0
HG2 F:GLN112 4.5 165.2 1.0
CD1 F:LEU56 4.5 162.8 1.0
N F:GLY72 4.5 159.9 1.0
HA2 F:GLY77 4.5 193.1 1.0
N F:CYS79 4.6 160.7 1.0
CA F:CYS79 4.6 156.4 1.0
HD22 F:LEU109 4.6 170.4 1.0
N F:GLY74 4.6 168.1 1.0
O F:CYS79 4.6 149.6 1.0
CB F:LEU109 4.7 138.2 1.0
HD11 F:LEU56 4.7 196.1 1.0
HA F:SER68 4.8 195.5 1.0
CA F:GLY74 4.8 168.6 1.0
H F:SER75 4.8 199.7 1.0
C F:GLY72 4.9 167.7 1.0
N F:GLY77 4.9 160.6 1.0
H F:ALA110 5.0 166.5 1.0
HA F:CYS111 5.0 170.6 1.0
HB2 F:LEU109 5.0 166.7 1.0

Reference:

G.Fritz, G.Fritz. N/A N/A.
ISSN: ESSN 1545-9985
Page generated: Fri Aug 9 17:26:06 2024

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