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Iron in PDB 1vlg: Crystal Structure of Ferritin (TM1128) From Thermotoga Maritima at 2.00 A Resolution

Protein crystallography data

The structure of Crystal Structure of Ferritin (TM1128) From Thermotoga Maritima at 2.00 A Resolution, PDB code: 1vlg was solved by Joint Center For Structural Genomics (Jcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 87.73 / 2.00
Space group H 3 2 1
Cell size a, b, c (Å), α, β, γ (°) 175.634, 175.634, 354.843, 90.00, 90.00, 120.00
R / Rfree (%) 17.8 / 21.8

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Ferritin (TM1128) From Thermotoga Maritima at 2.00 A Resolution (pdb code 1vlg). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Crystal Structure of Ferritin (TM1128) From Thermotoga Maritima at 2.00 A Resolution, PDB code: 1vlg:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 1vlg

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Iron binding site 1 out of 8 in the Crystal Structure of Ferritin (TM1128) From Thermotoga Maritima at 2.00 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Ferritin (TM1128) From Thermotoga Maritima at 2.00 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe200

b:38.5
occ:0.87
 OE1 A:GLU52 2.0 34.0 1.0
OE1 A:GLU19 2.3 31.1 1.0
O A:HOH254 2.3 30.6 1.0
ND1 A:HIS55 2.4 31.9 1.0
O A:HOH282 2.4 29.2 1.0
O A:HOH283 2.7 38.0 1.0
CD A:GLU52 3.1 34.1 1.0
CD A:GLU19 3.2 38.4 1.0
CE1 A:HIS55 3.2 27.2 1.0
OE2 A:GLU19 3.4 36.5 1.0
CG A:HIS55 3.5 24.9 1.0
OE2 A:GLU52 3.5 41.6 1.0
CB A:HIS55 3.8 22.8 1.0
OE1 A:GLN129 3.9 27.2 1.0
NE2 A:HIS55 4.4 23.1 1.0
CG A:GLU52 4.4 26.6 1.0
CG1 A:VAL99 4.4 29.8 1.0
OE1 A:GLU96 4.5 37.8 1.0
CG A:GLU19 4.5 26.1 1.0
CD2 A:HIS55 4.5 22.3 1.0
CA A:GLU52 4.6 24.4 1.0
OE2 A:GLU96 4.6 39.5 1.0
CB A:GLU52 4.7 26.6 1.0
CB A:GLU19 4.9 20.9 1.0
O A:GLU52 5.0 21.5 1.0
CD A:GLN129 5.0 27.2 1.0

Iron binding site 2 out of 8 in 1vlg

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Iron binding site 2 out of 8 in the Crystal Structure of Ferritin (TM1128) From Thermotoga Maritima at 2.00 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Ferritin (TM1128) From Thermotoga Maritima at 2.00 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe200

b:39.5
occ:0.87
 OE1 B:GLU52 2.0 33.9 1.0
OE1 B:GLU19 2.2 30.6 1.0
ND1 B:HIS55 2.4 28.6 1.0
O B:HOH286 2.4 31.9 1.0
O B:HOH308 2.4 27.4 1.0
O B:HOH309 2.6 32.4 1.0
CD B:GLU52 3.0 29.7 1.0
CD B:GLU19 3.1 36.9 1.0
CE1 B:HIS55 3.2 32.4 1.0
OE2 B:GLU52 3.4 32.9 1.0
OE2 B:GLU19 3.4 35.5 1.0
CG B:HIS55 3.5 24.5 1.0
CB B:HIS55 3.8 24.0 1.0
OE1 B:GLN129 4.1 26.4 1.0
CG B:GLU52 4.3 25.4 1.0
NE2 B:HIS55 4.4 27.7 1.0
CG1 B:VAL99 4.5 34.3 1.0
CG B:GLU19 4.5 24.1 1.0
CA B:GLU52 4.5 21.9 1.0
CD2 B:HIS55 4.5 19.0 1.0
CB B:GLU52 4.5 21.5 1.0
OE1 B:GLU96 4.6 34.8 1.0
OE2 B:GLU96 4.7 37.4 1.0
CB B:GLU19 4.8 21.8 1.0
OG B:SER22 4.9 28.3 1.0
CB B:SER22 5.0 21.5 1.0

Iron binding site 3 out of 8 in 1vlg

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Iron binding site 3 out of 8 in the Crystal Structure of Ferritin (TM1128) From Thermotoga Maritima at 2.00 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Ferritin (TM1128) From Thermotoga Maritima at 2.00 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe200

b:40.5
occ:0.90
 OE1 C:GLU52 2.0 30.6 1.0
OE1 C:GLU19 2.2 29.3 1.0
O C:HOH270 2.3 28.9 1.0
ND1 C:HIS55 2.4 29.7 1.0
O C:HOH264 2.7 40.8 1.0
O C:HOH263 2.7 38.6 1.0
CD C:GLU52 3.0 30.2 1.0
CD C:GLU19 3.1 30.9 1.0
CE1 C:HIS55 3.3 31.8 1.0
OE2 C:GLU52 3.3 36.1 1.0
OE2 C:GLU19 3.4 39.7 1.0
CG C:HIS55 3.5 26.1 1.0
CB C:HIS55 3.8 25.6 1.0
OE1 C:GLN129 4.1 26.9 1.0
CG C:GLU52 4.3 28.5 1.0
NE2 C:HIS55 4.5 26.4 1.0
CG1 C:VAL99 4.5 24.4 1.0
CG C:GLU19 4.5 24.4 1.0
OE1 C:GLU96 4.5 40.8 1.0
CA C:GLU52 4.5 21.1 1.0
CD2 C:HIS55 4.6 25.2 1.0
OE2 C:GLU96 4.6 37.4 1.0
CB C:GLU52 4.6 22.7 1.0
CB C:GLU19 4.9 21.5 1.0
O C:GLU52 4.9 19.2 1.0
OG C:SER22 5.0 26.0 1.0

Iron binding site 4 out of 8 in 1vlg

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Iron binding site 4 out of 8 in the Crystal Structure of Ferritin (TM1128) From Thermotoga Maritima at 2.00 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Ferritin (TM1128) From Thermotoga Maritima at 2.00 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe200

b:39.4
occ:0.86
 OE1 D:GLU52 2.0 28.2 1.0
O D:HOH260 2.3 30.0 1.0
OE1 D:GLU19 2.3 32.2 1.0
ND1 D:HIS55 2.4 32.0 1.0
O D:HOH262 2.4 30.4 1.0
O D:HOH247 2.8 36.6 1.0
CD D:GLU52 3.0 29.9 1.0
CE1 D:HIS55 3.2 25.4 1.0
CD D:GLU19 3.2 34.0 1.0
OE2 D:GLU52 3.4 34.1 1.0
CG D:HIS55 3.5 25.7 1.0
OE2 D:GLU19 3.5 34.3 1.0
CB D:HIS55 3.8 22.8 1.0
OE1 D:GLN129 4.1 29.2 1.0
CG D:GLU52 4.3 28.6 1.0
NE2 D:HIS55 4.4 26.8 1.0
CA D:GLU52 4.5 21.2 1.0
CG1 D:VAL99 4.5 26.6 1.0
CD2 D:HIS55 4.5 29.1 1.0
CB D:GLU52 4.6 22.8 1.0
CG D:GLU19 4.6 24.7 1.0
OE1 D:GLU96 4.7 38.2 1.0
OE2 D:GLU96 4.8 38.4 1.0
CB D:GLU19 4.9 20.5 1.0
O D:GLU52 5.0 24.1 1.0
OG D:SER22 5.0 27.0 1.0

Iron binding site 5 out of 8 in 1vlg

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Iron binding site 5 out of 8 in the Crystal Structure of Ferritin (TM1128) From Thermotoga Maritima at 2.00 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of Ferritin (TM1128) From Thermotoga Maritima at 2.00 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe200

b:50.2
occ:0.77
 OE1 E:GLU52 2.0 42.2 1.0
OE1 E:GLU19 2.3 35.4 1.0
O E:HOH297 2.4 28.2 1.0
O E:HOH320 2.6 33.2 1.0
ND1 E:HIS55 2.6 39.4 1.0
CD E:GLU52 3.0 32.9 1.0
CD E:GLU19 3.2 34.3 1.0
CE1 E:HIS55 3.4 32.5 1.0
OE2 E:GLU52 3.4 36.6 1.0
OE2 E:GLU19 3.5 34.2 1.0
CG E:HIS55 3.6 27.8 1.0
CB E:HIS55 3.9 21.6 1.0
OE1 E:GLN129 4.0 26.6 1.0
O E:HOH298 4.3 30.8 1.0
CG1 E:VAL99 4.3 27.4 1.0
CG E:GLU52 4.4 30.1 1.0
CG E:GLU19 4.6 25.4 1.0
NE2 E:HIS55 4.6 33.0 1.0
CA E:GLU52 4.6 20.3 1.0
CB E:GLU52 4.7 22.2 1.0
CD2 E:HIS55 4.7 25.8 1.0
OE1 E:GLU132 4.8 62.3 1.0
OE1 E:GLU96 4.9 34.6 1.0
CB E:GLU19 4.9 23.9 1.0
CD E:GLN129 5.0 28.4 1.0
OE2 E:GLU96 5.0 45.9 1.0

Iron binding site 6 out of 8 in 1vlg

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Iron binding site 6 out of 8 in the Crystal Structure of Ferritin (TM1128) From Thermotoga Maritima at 2.00 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of Ferritin (TM1128) From Thermotoga Maritima at 2.00 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe200

b:36.5
occ:0.90
 OE1 F:GLU52 2.0 33.5 1.0
OE1 F:GLU19 2.2 27.3 1.0
O F:HOH241 2.2 36.6 1.0
O F:HOH220 2.3 24.7 1.0
ND1 F:HIS55 2.4 26.9 1.0
O F:HOH259 2.7 34.2 1.0
CD F:GLU52 3.0 25.2 1.0
CD F:GLU19 3.2 33.7 1.0
CE1 F:HIS55 3.3 22.0 1.0
OE2 F:GLU52 3.3 27.7 1.0
OE2 F:GLU19 3.5 32.5 1.0
CG F:HIS55 3.5 22.7 1.0
CB F:HIS55 3.9 24.4 1.0
OE1 F:GLN129 4.1 26.3 1.0
CG F:GLU52 4.3 26.1 1.0
CG1 F:VAL99 4.4 23.5 1.0
NE2 F:HIS55 4.4 27.2 1.0
OE1 F:GLU96 4.5 35.8 1.0
CG F:GLU19 4.5 24.6 1.0
CA F:GLU52 4.5 20.6 1.0
OE2 F:GLU96 4.5 40.7 1.0
CD2 F:HIS55 4.6 22.1 1.0
CB F:GLU52 4.6 22.5 1.0
CB F:GLU19 4.8 19.4 1.0
CD F:GLU96 5.0 34.2 1.0
CB F:SER22 5.0 19.4 1.0

Iron binding site 7 out of 8 in 1vlg

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Iron binding site 7 out of 8 in the Crystal Structure of Ferritin (TM1128) From Thermotoga Maritima at 2.00 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of Ferritin (TM1128) From Thermotoga Maritima at 2.00 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe200

b:42.5
occ:0.87
 OE1 G:GLU52 2.0 32.7 1.0
OE1 G:GLU19 2.2 31.8 1.0
O G:HOH238 2.4 31.1 1.0
ND1 G:HIS55 2.4 31.6 1.0
CD G:GLU52 3.0 36.2 1.0
CD G:GLU19 3.2 32.5 1.0
CE1 G:HIS55 3.2 28.6 1.0
OE2 G:GLU52 3.4 39.5 1.0
OE2 G:GLU19 3.4 39.1 1.0
CG G:HIS55 3.6 24.9 1.0
CB G:HIS55 4.0 22.3 1.0
OE1 G:GLN129 4.0 28.6 1.0
CG G:GLU52 4.3 25.6 1.0
NE2 G:HIS55 4.4 26.8 1.0
CA G:GLU52 4.5 23.9 1.0
CG1 G:VAL99 4.5 24.4 1.0
CG G:GLU19 4.5 24.9 1.0
CD2 G:HIS55 4.6 26.0 1.0
CB G:GLU52 4.6 24.9 1.0
OE2 G:GLU96 4.6 44.9 1.0
OE1 G:GLU96 4.7 37.6 1.0
OE2 G:GLU132 4.8 61.1 1.0
CB G:GLU19 4.9 19.0 1.0
OG G:SER22 5.0 28.1 1.0

Iron binding site 8 out of 8 in 1vlg

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Iron binding site 8 out of 8 in the Crystal Structure of Ferritin (TM1128) From Thermotoga Maritima at 2.00 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of Ferritin (TM1128) From Thermotoga Maritima at 2.00 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe200

b:50.2
occ:0.95
 OE1 H:GLU52 1.9 32.6 1.0
OE1 H:GLU19 2.3 42.0 1.0
O H:HOH238 2.4 39.3 1.0
ND1 H:HIS55 2.4 30.4 1.0
O H:HOH237 2.6 38.2 1.0
CD H:GLU52 3.0 27.6 1.0
CD H:GLU19 3.2 37.3 1.0
CE1 H:HIS55 3.2 30.6 1.0
OE2 H:GLU19 3.4 36.1 1.0
OE2 H:GLU52 3.5 29.4 1.0
CG H:HIS55 3.5 25.2 1.0
CB H:HIS55 3.9 24.6 1.0
OE1 H:GLN129 4.1 23.9 1.0
CG H:GLU52 4.3 22.8 1.0
NE2 H:HIS55 4.4 28.4 1.0
CG1 H:VAL99 4.4 24.2 1.0
CB H:GLU52 4.4 23.0 1.0
CA H:GLU52 4.5 22.3 1.0
CD2 H:HIS55 4.6 29.8 1.0
CG H:GLU19 4.6 28.8 1.0
OE1 H:GLU96 4.6 37.2 1.0
OE2 H:GLU96 4.6 39.5 1.0
OE1 H:GLU132 5.0 44.1 1.0

Reference:

Joint Center For Structural Genomics (Jcsg), Joint Center For Structural Genomics (Jcsg). N/A N/A.
Page generated: Sat Aug 3 16:14:47 2024

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