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Iron in PDB 6txj: Crystal Structure of Thermotoga Maritima A42V E65D Ferritin

Enzymatic activity of Crystal Structure of Thermotoga Maritima A42V E65D Ferritin

All present enzymatic activity of Crystal Structure of Thermotoga Maritima A42V E65D Ferritin:
1.16.3.2;

Protein crystallography data

The structure of Crystal Structure of Thermotoga Maritima A42V E65D Ferritin, PDB code: 6txj was solved by P.Wilk, P.Grudnik, M.Kumar, J.Heddle, S.Chakraborti, A.P.Biela, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.86 / 2.17
Space group H 3 2 1
Cell size a, b, c (Å), α, β, γ (°) 176.203, 176.203, 352.794, 90, 90, 120
R / Rfree (%) 21 / 24.6

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Thermotoga Maritima A42V E65D Ferritin (pdb code 6txj). 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 Thermotoga Maritima A42V E65D Ferritin, PDB code: 6txj:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 6txj

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Iron binding site 1 out of 8 in the Crystal Structure of Thermotoga Maritima A42V E65D Ferritin


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 Thermotoga Maritima A42V E65D Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe208

b:45.4
occ:0.27
 OE2 A:GLU19 1.7 91.4 1.0
OE1 A:GLU52 1.9 92.1 1.0
ND1 A:HIS55 2.1 89.4 1.0
O A:HOH304 2.3 65.4 1.0
CD A:GLU52 2.9 86.8 1.0
CD A:GLU19 2.9 88.2 1.0
CE1 A:HIS55 3.0 85.5 1.0
OE2 A:GLU52 3.2 89.5 1.0
CG A:HIS55 3.2 81.9 1.0
CG A:GLU19 3.6 85.3 1.0
CB A:HIS55 3.6 72.4 1.0
OE1 A:GLU19 3.8 88.9 1.0
OE1 A:GLN129 4.0 74.0 1.0
NE2 A:HIS55 4.1 85.0 1.0
CG A:GLU52 4.2 79.9 1.0
CD2 A:HIS55 4.3 83.8 1.0
OE1 A:GLU132 4.3 104.2 1.0
CG1 A:VAL99 4.4 59.6 1.0
CB A:GLU52 4.5 72.1 1.0
CA A:GLU52 4.5 69.5 1.0
OE2 A:GLU96 4.9 82.9 1.0

Iron binding site 2 out of 8 in 6txj

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Iron binding site 2 out of 8 in the Crystal Structure of Thermotoga Maritima A42V E65D Ferritin


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 Thermotoga Maritima A42V E65D Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe212

b:78.0
occ:1.00
 OE2 B:GLU52 2.0 97.7 1.0
O B:HOH319 2.2 69.5 1.0
ND1 B:HIS55 2.2 67.1 1.0
OE1 B:GLU19 2.3 69.1 1.0
O B:HOH312 2.5 79.5 1.0
O B:HOH306 2.5 71.8 1.0
CE1 B:HIS55 3.1 69.0 1.0
CD B:GLU52 3.1 89.3 1.0
CD B:GLU19 3.2 64.6 1.0
CG B:HIS55 3.3 67.6 1.0
OE2 B:GLU19 3.4 64.5 1.0
OE1 B:GLU52 3.5 91.7 1.0
CB B:HIS55 3.8 59.3 1.0
OE1 B:GLN129 4.1 65.4 1.0
NE2 B:HIS55 4.3 68.5 1.0
CG B:GLU52 4.4 81.3 1.0
CD2 B:HIS55 4.4 65.7 1.0
OE1 B:GLU96 4.4 75.3 1.0
CG1 B:VAL99 4.5 56.0 1.0
OE2 B:GLU96 4.5 75.5 1.0
CG B:GLU19 4.6 60.3 1.0
CA B:GLU52 4.6 66.3 1.0
CB B:GLU52 4.6 74.9 1.0
OG B:SER22 4.9 62.9 1.0
CD B:GLU96 4.9 71.6 1.0
CB B:GLU19 5.0 60.1 1.0

Iron binding site 3 out of 8 in 6txj

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Iron binding site 3 out of 8 in the Crystal Structure of Thermotoga Maritima A42V E65D Ferritin


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 Thermotoga Maritima A42V E65D Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe205

b:86.5
occ:1.00
 OE1 C:GLU52 2.0 126.2 1.0
O C:HOH302 2.3 71.8 1.0
OE1 C:GLU19 2.5 90.1 1.0
ND1 C:HIS55 2.5 85.2 1.0
CD C:GLU52 2.8 111.8 1.0
OE2 C:GLU52 3.1 116.8 1.0
CE1 C:HIS55 3.3 85.9 1.0
CD C:GLU19 3.3 87.5 1.0
OE2 C:GLU19 3.5 89.8 1.0
CG C:HIS55 3.5 85.4 1.0
OE1 C:GLN129 3.9 92.5 1.0
CB C:HIS55 3.9 84.5 1.0
OE2 C:GLU96 4.0 100.5 1.0
OE1 C:GLU96 4.1 98.9 1.0
CG C:GLU52 4.2 98.1 1.0
NE2 C:HIS55 4.5 85.8 1.0
CD C:GLU96 4.5 97.3 1.0
CA C:GLU52 4.5 87.2 1.0
CG1 C:VAL99 4.6 86.7 1.0
CB C:GLU52 4.6 91.0 1.0
CD2 C:HIS55 4.6 85.3 1.0
CG C:GLU19 4.7 81.7 1.0
OE1 C:GLU132 4.9 102.5 1.0
CD C:GLN129 5.0 89.3 1.0
OG C:SER22 5.0 96.9 1.0

Iron binding site 4 out of 8 in 6txj

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Iron binding site 4 out of 8 in the Crystal Structure of Thermotoga Maritima A42V E65D Ferritin


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 Thermotoga Maritima A42V E65D Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe206

b:73.9
occ:0.77
 OE1 D:GLU52 2.0 114.0 1.0
OE1 D:GLU19 2.2 85.2 1.0
ND1 D:HIS55 2.3 77.7 1.0
O D:HOH301 2.6 88.6 1.0
CD D:GLU52 2.9 102.2 1.0
CD D:GLU19 3.1 78.6 1.0
CE1 D:HIS55 3.1 76.4 1.0
OE2 D:GLU52 3.1 105.6 1.0
OE2 D:GLU19 3.3 78.1 1.0
CG D:HIS55 3.3 77.9 1.0
OE1 D:GLN129 3.7 73.6 1.0
CB D:HIS55 3.7 73.8 1.0
NE2 D:HIS55 4.3 76.1 1.0
CG D:GLU52 4.3 91.7 1.0
CG1 D:VAL99 4.4 72.1 1.0
OE1 D:GLU96 4.4 83.0 1.0
CD2 D:HIS55 4.4 76.6 1.0
CG D:GLU19 4.5 74.1 1.0
OE2 D:GLU96 4.7 79.7 1.0
CB D:GLU52 4.8 83.2 1.0
CA D:GLU52 4.8 79.6 1.0
CD D:GLN129 4.9 73.6 1.0
CB D:GLU19 4.9 72.0 1.0

Iron binding site 5 out of 8 in 6txj

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Iron binding site 5 out of 8 in the Crystal Structure of Thermotoga Maritima A42V E65D Ferritin


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 Thermotoga Maritima A42V E65D Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe204

b:46.0
occ:0.34
 OE1 E:GLU52 1.7 100.5 1.0
O E:HOH301 1.8 60.6 1.0
O E:HOH308 1.9 59.8 1.0
OE1 E:GLU19 2.1 97.7 1.0
ND1 E:HIS55 2.2 90.7 1.0
CD E:GLU52 2.7 93.5 1.0
OE2 E:GLU52 3.0 95.7 1.0
CD E:GLU19 3.1 94.5 1.0
CE1 E:HIS55 3.2 91.2 1.0
CG E:HIS55 3.2 89.4 1.0
OE2 E:GLU19 3.5 95.1 1.0
CB E:HIS55 3.5 84.8 1.0
CG E:GLU52 4.0 86.1 1.0
NE2 E:GLN129 4.2 83.3 1.0
NE2 E:HIS55 4.3 90.7 1.0
CA E:GLU52 4.3 81.7 1.0
CD2 E:HIS55 4.3 90.1 1.0
CB E:GLU52 4.4 82.5 1.0
OE2 E:GLU96 4.4 86.7 1.0
CG E:GLU19 4.5 89.6 1.0
OG E:SER22 4.7 87.4 1.0
OE1 E:GLU96 4.7 85.5 1.0
CB E:SER22 4.7 81.8 1.0
CB E:GLU19 4.8 85.0 1.0
O E:GLU52 4.8 77.8 1.0
CD E:GLU96 5.0 84.9 1.0

Iron binding site 6 out of 8 in 6txj

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Iron binding site 6 out of 8 in the Crystal Structure of Thermotoga Maritima A42V E65D Ferritin


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 Thermotoga Maritima A42V E65D Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe207

b:79.4
occ:0.78
 OE1 F:GLU52 2.0 110.6 1.0
ND1 F:HIS55 2.2 88.7 1.0
OE1 F:GLU19 2.3 85.0 1.0
CD F:GLU52 2.8 94.3 1.0
OE2 F:GLU52 3.0 100.0 1.0
CD F:GLU19 3.0 83.5 1.0
CE1 F:HIS55 3.1 87.3 1.0
OE2 F:GLU19 3.1 84.5 1.0
CG F:HIS55 3.3 86.3 1.0
OE1 F:GLN129 3.6 86.1 1.0
CB F:HIS55 3.7 81.6 1.0
OE2 F:GLU96 4.2 99.8 1.0
CG F:GLU52 4.3 76.8 1.0
NE2 F:HIS55 4.3 87.5 1.0
CG1 F:VAL99 4.3 71.1 1.0
CD2 F:HIS55 4.4 87.0 1.0
CG F:GLU19 4.5 81.5 1.0
OE1 F:GLU96 4.7 99.5 1.0
CB F:GLU52 4.7 74.8 1.0
CD F:GLN129 4.8 84.5 1.0
CA F:GLU52 4.8 77.0 1.0
OE2 F:GLU132 4.8 96.0 1.0
CD F:GLU96 4.9 97.6 1.0

Iron binding site 7 out of 8 in 6txj

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Iron binding site 7 out of 8 in the Crystal Structure of Thermotoga Maritima A42V E65D Ferritin


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 Thermotoga Maritima A42V E65D Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe207

b:62.6
occ:0.52
 OE1 G:GLU52 1.9 113.5 1.0
OE1 G:GLU19 2.0 112.7 1.0
O G:HOH301 2.0 64.0 1.0
ND1 G:HIS55 2.2 110.7 1.0
CD G:GLU19 2.8 104.3 1.0
CD G:GLU52 2.9 105.2 1.0
OE2 G:GLU19 2.9 107.4 1.0
CE1 G:HIS55 3.1 108.8 1.0
OE2 G:GLU52 3.2 107.8 1.0
CG G:HIS55 3.3 105.6 1.0
CB G:HIS55 3.6 95.0 1.0
OE2 G:GLU96 3.9 112.3 1.0
NE2 G:GLN129 3.9 97.3 1.0
CG G:GLU52 4.2 96.9 1.0
CG G:GLU19 4.2 95.4 1.0
NE2 G:HIS55 4.2 108.6 1.0
CD2 G:HIS55 4.3 108.0 1.0
CA G:GLU52 4.5 91.5 1.0
CB G:GLU52 4.5 91.5 1.0
CB G:GLU19 4.7 90.8 1.0
CG2 G:VAL99 4.8 94.0 1.0
CD G:GLN129 4.9 95.3 1.0

Iron binding site 8 out of 8 in 6txj

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Iron binding site 8 out of 8 in the Crystal Structure of Thermotoga Maritima A42V E65D Ferritin


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 Thermotoga Maritima A42V E65D Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe205

b:65.7
occ:0.49
 OE1 H:GLU19 2.1 110.4 1.0
OE1 H:GLU52 2.1 108.8 1.0
O H:HOH301 2.2 72.1 1.0
ND1 H:HIS55 2.2 100.8 1.0
CD H:GLU19 2.8 101.9 1.0
OE2 H:GLU19 3.0 102.8 1.0
CD H:GLU52 3.1 101.8 1.0
CE1 H:HIS55 3.1 97.7 1.0
CG H:HIS55 3.2 95.9 1.0
OE2 H:GLU52 3.4 105.4 1.0
CB H:HIS55 3.5 88.4 1.0
OE1 H:GLN129 4.1 89.1 1.0
CG H:GLU19 4.2 95.1 1.0
NE2 H:HIS55 4.2 97.9 1.0
CD2 H:HIS55 4.3 97.9 1.0
CG H:GLU52 4.4 92.7 1.0
CG1 H:VAL99 4.4 82.3 1.0
OE2 H:GLU96 4.6 99.2 1.0
OG H:SER22 4.6 98.9 1.0
CA H:GLU52 4.6 88.7 1.0
CB H:GLU52 4.6 89.0 1.0
CB H:GLU19 4.8 89.6 1.0
OE1 H:GLU96 4.8 94.0 1.0
O H:GLU52 5.0 83.5 1.0

Reference:

P.Wilk, P.Grudnik, M.Kumar, J.Heddle, S.Chakraborti, A.P.Biela. Crystal Structure of Thermotoga Maritima Ferritin in Apo Form To Be Published.
Page generated: Wed Aug 7 11:50:17 2024

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