Iron in PDB 8d5v: WHIB6 Bound to the SIGMAAR4-Rnap Beta Flap Tip Chimera

Enzymatic activity of WHIB6 Bound to the SIGMAAR4-Rnap Beta Flap Tip Chimera

All present enzymatic activity of WHIB6 Bound to the SIGMAAR4-Rnap Beta Flap Tip Chimera:
2.7.7.6;

Protein crystallography data

The structure of WHIB6 Bound to the SIGMAAR4-Rnap Beta Flap Tip Chimera, PDB code: 8d5v was solved by T.Wan, L.M.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.27 / 1.80
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 62.983, 66.54, 158.805, 90, 90, 90
R / Rfree (%) 21 / 23.1

Iron Binding Sites:

The binding sites of Iron atom in the WHIB6 Bound to the SIGMAAR4-Rnap Beta Flap Tip Chimera (pdb code 8d5v). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the WHIB6 Bound to the SIGMAAR4-Rnap Beta Flap Tip Chimera, PDB code: 8d5v:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 8d5v

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Iron binding site 1 out of 8 in the WHIB6 Bound to the SIGMAAR4-Rnap Beta Flap Tip Chimera


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of WHIB6 Bound to the SIGMAAR4-Rnap Beta Flap Tip Chimera within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:38.3
occ:1.00
 FE1 A:SF4201 0.0 38.3 1.0
S4 A:SF4201 2.3 37.2 1.0
S2 A:SF4201 2.3 35.9 1.0
SG A:CYS14 2.3 33.4 1.0
S3 A:SF4201 2.3 38.0 1.0
FE3 A:SF4201 2.7 33.8 1.0
FE2 A:SF4201 2.7 42.7 1.0
FE4 A:SF4201 2.7 32.8 1.0
CB A:CYS14 3.2 34.0 1.0
S1 A:SF4201 3.9 37.7 1.0
N A:CYS14 4.2 38.0 1.0
CA A:GLY12 4.2 45.8 1.0
NE1 A:TRP21 4.2 34.9 1.0
CA A:CYS14 4.3 36.5 1.0
CD1 A:TRP21 4.3 32.5 1.0
CE1 B:HIS516 4.4 41.3 1.0
C A:GLY12 4.6 46.2 1.0
CG B:PRO517 4.6 41.1 1.0
SG A:CYS42 4.8 32.1 1.0
N A:VAL13 4.8 43.5 1.0
SG A:CYS33 4.8 35.1 1.0
SG A:CYS36 4.8 39.9 1.0
CE2 A:TRP21 4.9 36.1 1.0
CB B:PRO517 4.9 40.0 1.0
NE2 B:HIS516 5.0 42.7 1.0

Iron binding site 2 out of 8 in 8d5v

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Iron binding site 2 out of 8 in the WHIB6 Bound to the SIGMAAR4-Rnap Beta Flap Tip Chimera


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of WHIB6 Bound to the SIGMAAR4-Rnap Beta Flap Tip Chimera within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:42.7
occ:1.00
 FE2 A:SF4201 0.0 42.7 1.0
S3 A:SF4201 2.3 38.0 1.0
SG A:CYS36 2.3 39.9 1.0
S1 A:SF4201 2.3 37.7 1.0
S4 A:SF4201 2.3 37.2 1.0
FE4 A:SF4201 2.7 32.8 1.0
FE1 A:SF4201 2.7 38.3 1.0
FE3 A:SF4201 2.7 33.8 1.0
CB A:CYS36 3.1 39.7 1.0
S2 A:SF4201 3.9 35.9 1.0
CA A:GLY12 4.0 45.8 1.0
CG A:ARG38 4.2 47.9 1.0
O A:HOH323 4.3 43.2 1.0
CA A:CYS36 4.6 42.3 1.0
SG A:CYS14 4.8 33.4 1.0
CA A:CYS33 4.8 38.8 1.0
SG A:CYS42 4.8 32.1 1.0
SG A:CYS33 4.8 35.1 1.0
CB A:CYS42 4.9 33.1 1.0
N A:ARG39 4.9 37.5 1.0
CA A:ARG39 4.9 35.3 1.0
C A:GLY12 4.9 46.2 1.0
C A:ARG38 4.9 45.3 1.0
CD A:ARG38 5.0 50.0 1.0
N A:GLY12 5.0 47.4 1.0
N A:VAL13 5.0 43.5 1.0

Iron binding site 3 out of 8 in 8d5v

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Iron binding site 3 out of 8 in the WHIB6 Bound to the SIGMAAR4-Rnap Beta Flap Tip Chimera


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of WHIB6 Bound to the SIGMAAR4-Rnap Beta Flap Tip Chimera within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:33.8
occ:1.00
 FE3 A:SF4201 0.0 33.8 1.0
S4 A:SF4201 2.3 37.2 1.0
S2 A:SF4201 2.3 35.9 1.0
SG A:CYS33 2.3 35.1 1.0
S1 A:SF4201 2.3 37.7 1.0
FE1 A:SF4201 2.7 38.3 1.0
FE2 A:SF4201 2.7 42.7 1.0
FE4 A:SF4201 2.8 32.8 1.0
CB A:CYS33 3.3 36.8 1.0
NE1 A:TRP21 3.6 34.9 1.0
CA A:CYS33 3.6 38.8 1.0
S3 A:SF4201 3.9 38.0 1.0
CD1 A:TRP21 3.9 32.5 1.0
N A:ALA57 4.0 31.8 1.0
N A:CYS33 4.5 41.0 1.0
CA A:ALA57 4.5 31.9 1.0
CB A:CYS36 4.6 39.7 1.0
SG A:CYS36 4.7 39.9 1.0
CE2 A:TRP21 4.7 36.1 1.0
SG A:CYS42 4.7 32.1 1.0
N A:GLY58 4.7 30.2 1.0
C A:CYS33 4.8 40.3 1.0
SG A:CYS14 4.8 33.4 1.0
O A:CYS33 4.9 39.6 1.0
CB A:CYS14 4.9 34.0 1.0

Iron binding site 4 out of 8 in 8d5v

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Iron binding site 4 out of 8 in the WHIB6 Bound to the SIGMAAR4-Rnap Beta Flap Tip Chimera


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of WHIB6 Bound to the SIGMAAR4-Rnap Beta Flap Tip Chimera within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:32.8
occ:1.00
 FE4 A:SF4201 0.0 32.8 1.0
S3 A:SF4201 2.2 38.0 1.0
SG A:CYS42 2.3 32.1 1.0
S1 A:SF4201 2.3 37.7 1.0
S2 A:SF4201 2.4 35.9 1.0
FE2 A:SF4201 2.7 42.7 1.0
FE1 A:SF4201 2.7 38.3 1.0
FE3 A:SF4201 2.8 33.8 1.0
CB A:CYS42 3.0 33.1 1.0
N A:ALA57 3.9 31.8 1.0
S4 A:SF4201 3.9 37.2 1.0
CG B:PRO517 4.1 41.1 1.0
CA A:ALA57 4.5 31.9 1.0
CA A:CYS42 4.5 34.6 1.0
NH1 A:ARG38 4.6 46.3 1.0
SG A:CYS14 4.8 33.4 1.0
SG A:CYS36 4.8 39.9 1.0
SG A:CYS33 4.8 35.1 1.0
CA A:TRP56 4.9 31.8 1.0
C A:TRP56 4.9 31.6 1.0
CB B:PRO517 4.9 40.0 1.0

Iron binding site 5 out of 8 in 8d5v

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Iron binding site 5 out of 8 in the WHIB6 Bound to the SIGMAAR4-Rnap Beta Flap Tip Chimera


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of WHIB6 Bound to the SIGMAAR4-Rnap Beta Flap Tip Chimera within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:50.0
occ:1.00
 FE1 C:SF4201 0.0 50.0 1.0
S3 C:SF4201 2.2 48.9 1.0
S2 C:SF4201 2.3 51.6 1.0
S4 C:SF4201 2.3 48.3 1.0
SG C:CYS14 2.4 48.8 1.0
FE2 C:SF4201 2.6 46.5 1.0
FE4 C:SF4201 2.7 45.7 1.0
FE3 C:SF4201 2.7 48.4 1.0
CB C:CYS14 3.2 53.3 1.0
S1 C:SF4201 3.9 47.2 1.0
N C:CYS14 4.1 57.8 1.0
CA C:CYS14 4.3 58.1 1.0
NE1 C:TRP21 4.4 61.7 1.0
CG D:PRO517 4.5 47.0 1.0
CA C:GLY12 4.5 49.7 1.0
CD1 C:TRP21 4.5 61.0 1.0
CE1 D:HIS516 4.5 48.9 1.0
C C:GLY12 4.7 53.5 1.0
CB D:PRO517 4.8 46.3 1.0
SG C:CYS36 4.8 51.5 1.0
SG C:CYS42 4.8 45.5 1.0
NE2 D:GLN521 4.8 61.6 1.0
N C:VAL13 4.8 60.1 1.0
SG C:CYS33 4.9 52.7 1.0

Iron binding site 6 out of 8 in 8d5v

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Iron binding site 6 out of 8 in the WHIB6 Bound to the SIGMAAR4-Rnap Beta Flap Tip Chimera


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of WHIB6 Bound to the SIGMAAR4-Rnap Beta Flap Tip Chimera within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:46.5
occ:1.00
 FE2 C:SF4201 0.0 46.5 1.0
S4 C:SF4201 2.2 48.3 1.0
S1 C:SF4201 2.3 47.2 1.0
S3 C:SF4201 2.3 48.9 1.0
SG C:CYS36 2.3 51.5 1.0
FE1 C:SF4201 2.6 50.0 1.0
FE3 C:SF4201 2.7 48.4 1.0
FE4 C:SF4201 2.7 45.7 1.0
CB C:CYS36 3.2 52.2 1.0
S2 C:SF4201 3.8 51.6 1.0
CA C:GLY12 4.3 49.7 1.0
CG C:ARG38 4.3 56.1 1.0
CA C:CYS36 4.7 53.9 1.0
SG C:CYS14 4.8 48.8 1.0
CA C:CYS33 4.8 53.1 1.0
SG C:CYS42 4.8 45.5 1.0
SG C:CYS33 4.9 52.7 1.0
CB C:CYS42 4.9 44.3 1.0
CD C:ARG38 4.9 59.2 1.0
N C:VAL13 4.9 60.1 1.0

Iron binding site 7 out of 8 in 8d5v

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Iron binding site 7 out of 8 in the WHIB6 Bound to the SIGMAAR4-Rnap Beta Flap Tip Chimera


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of WHIB6 Bound to the SIGMAAR4-Rnap Beta Flap Tip Chimera within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:48.4
occ:1.00
 FE3 C:SF4201 0.0 48.4 1.0
S2 C:SF4201 2.2 51.6 1.0
S4 C:SF4201 2.3 48.3 1.0
S1 C:SF4201 2.3 47.2 1.0
SG C:CYS33 2.4 52.7 1.0
FE2 C:SF4201 2.7 46.5 1.0
FE1 C:SF4201 2.7 50.0 1.0
FE4 C:SF4201 2.7 45.7 1.0
CB C:CYS33 3.4 52.0 1.0
CA C:CYS33 3.7 53.1 1.0
NE1 C:TRP21 3.8 61.7 1.0
S3 C:SF4201 3.9 48.9 1.0
N C:ALA57 4.0 50.3 1.0
CD1 C:TRP21 4.2 61.0 1.0
CA C:ALA57 4.4 47.8 1.0
N C:CYS33 4.5 56.6 1.0
N C:GLY58 4.6 46.9 1.0
SG C:CYS36 4.7 51.5 1.0
CB C:CYS36 4.7 52.2 1.0
SG C:CYS42 4.8 45.5 1.0
C C:CYS33 4.8 52.4 1.0
O C:LEU55 4.8 50.4 1.0
SG C:CYS14 4.9 48.8 1.0
O C:CYS33 4.9 50.1 1.0
CE2 C:TRP21 5.0 65.4 1.0
C C:TRP56 5.0 43.9 1.0
C C:ALA57 5.0 50.4 1.0

Iron binding site 8 out of 8 in 8d5v

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Iron binding site 8 out of 8 in the WHIB6 Bound to the SIGMAAR4-Rnap Beta Flap Tip Chimera


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of WHIB6 Bound to the SIGMAAR4-Rnap Beta Flap Tip Chimera within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:45.7
occ:1.00
 FE4 C:SF4201 0.0 45.7 1.0
S2 C:SF4201 2.3 51.6 1.0
S3 C:SF4201 2.3 48.9 1.0
SG C:CYS42 2.3 45.5 1.0
S1 C:SF4201 2.3 47.2 1.0
FE1 C:SF4201 2.7 50.0 1.0
FE3 C:SF4201 2.7 48.4 1.0
FE2 C:SF4201 2.7 46.5 1.0
CB C:CYS42 3.1 44.3 1.0
N C:ALA57 3.8 50.3 1.0
S4 C:SF4201 3.9 48.3 1.0
CG D:PRO517 4.0 47.0 1.0
CA C:ALA57 4.4 47.8 1.0
CA C:CYS42 4.6 42.2 1.0
NH1 C:ARG38 4.6 58.9 1.0
CA C:TRP56 4.8 45.7 1.0
C C:TRP56 4.8 43.9 1.0
CB D:PRO517 4.8 46.3 1.0
SG C:CYS14 4.8 48.8 1.0
SG C:CYS33 4.8 52.7 1.0
SG C:CYS36 4.8 51.5 1.0

Reference:

T.Wan, L.M.Zhang. Crystal Structure of WHIB6 and SIGA4-Betatip Complex To Be Published.
Page generated: Thu Jul 27 16:35:22 2023

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