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Iron in PDB 7w5e: Oxidase Chap D49L Mutant

Protein crystallography data

The structure of Oxidase Chap D49L Mutant, PDB code: 7w5e was solved by Y.Wang, W.Zheng, Z.Meng, Y.Jin, J.Zhu, R.Tan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.41 / 1.65
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 40.76, 62.07, 92.02, 90, 91.8, 90
R / Rfree (%) 20.4 / 23.8

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Iron atom in the Oxidase Chap D49L Mutant (pdb code 7w5e). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 13 binding sites of Iron where determined in the Oxidase Chap D49L Mutant, PDB code: 7w5e:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 13 in 7w5e

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Iron binding site 1 out of 13 in the Oxidase Chap D49L Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Oxidase Chap D49L Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:20.1
occ:1.00
 OE1 A:GLU119 2.0 29.0 1.0
NE2 A:HIS63 2.1 22.1 1.0
NE2 D:HIS7 2.2 21.5 1.0
O B:HOH330 2.3 23.4 1.0
O A:HOH311 2.4 42.2 1.0
CD A:GLU119 2.7 23.6 1.0
OE2 A:GLU119 2.7 35.5 1.0
CD2 A:HIS63 3.1 18.8 1.0
CE1 A:HIS63 3.1 22.5 1.0
CE1 D:HIS7 3.1 21.1 1.0
CD2 D:HIS7 3.2 18.3 1.0
OH A:TYR109 3.7 41.1 1.0
CB A:ALA65 4.0 19.2 1.0
CE2 A:TYR109 4.0 24.6 1.0
O A:HOH384 4.0 43.5 1.0
CG A:GLU119 4.1 25.4 1.0
ND1 A:HIS63 4.2 23.3 1.0
CG A:HIS63 4.3 19.9 1.0
CZ A:TYR109 4.3 29.4 1.0
ND1 D:HIS7 4.3 19.5 1.0
CG D:HIS7 4.4 17.5 1.0
O B:HOH417 4.4 31.8 1.0
CE1 B:TYR125 4.6 27.1 1.0
CB A:GLU119 4.6 19.9 1.0
O A:HOH402 4.7 46.2 1.0
OE1 A:GLN91 4.7 32.0 1.0
OH B:TYR125 4.9 31.5 1.0

Iron binding site 2 out of 13 in 7w5e

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Iron binding site 2 out of 13 in the Oxidase Chap D49L Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Oxidase Chap D49L Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe202

b:12.8
occ:1.00
 OD2 A:ASP45 1.9 18.1 1.0
OE1 A:GLU4 2.0 11.8 1.0
CE1 C:HIS0 2.1 26.1 1.0
O C:HOH322 2.2 15.7 1.0
OE2 A:GLU4 2.5 16.4 1.0
NE2 C:HIS0 2.5 24.8 1.0
CD A:GLU4 2.5 14.2 1.0
CG A:ASP45 2.9 13.2 1.0
CB A:ASP45 3.3 13.2 1.0
ND1 C:HIS0 3.3 30.4 1.0
CD2 C:HIS0 3.7 32.3 1.0
O C:MET1 3.8 22.9 1.0
CG A:GLU4 4.0 12.9 1.0
OD1 A:ASP45 4.1 20.0 1.0
O A:HOH334 4.1 16.1 1.0
CG C:HIS0 4.1 30.6 1.0
O A:HOH395 4.2 15.6 1.0
CD2 D:LEU67 4.4 10.2 1.0
O A:HOH388 4.6 36.6 1.0
CB A:GLU4 4.7 10.4 1.0
C C:MET1 4.7 25.7 1.0
CA A:ASP45 4.8 10.4 1.0
CB D:ASN44 4.9 13.0 1.0

Iron binding site 3 out of 13 in 7w5e

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Iron binding site 3 out of 13 in the Oxidase Chap D49L Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Oxidase Chap D49L Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe203

b:18.3
occ:1.00
 O A:HOH396 2.0 18.1 1.0
O A:HOH336 2.1 25.1 1.0
NE2 A:HIS116 2.1 27.2 1.0
SG A:CYS64 2.3 19.3 1.0
CD2 A:HIS116 3.1 27.0 1.0
CE1 A:HIS116 3.1 27.7 1.0
CB A:CYS64 3.4 18.8 1.0
N A:CYS64 3.5 17.1 1.0
C A:HIS63 3.8 21.5 1.0
O A:HOH390 3.8 34.6 1.0
CA A:CYS64 3.9 16.5 1.0
O A:HIS63 4.1 18.2 1.0
OD2 A:ASP58 4.1 20.9 1.0
O D:HOH374 4.1 24.3 1.0
O A:ASN117 4.1 21.9 1.0
O D:HOH329 4.1 19.6 1.0
ND1 A:HIS116 4.2 27.4 1.0
CG A:HIS116 4.2 22.3 1.0
OG1 D:THR8 4.3 19.6 1.0
CG2 A:VAL10 4.3 20.7 1.0
CG1 A:VAL10 4.3 20.3 1.0
CA A:HIS63 4.4 16.4 1.0
CG A:ASP58 4.9 34.4 1.0
CB A:VAL10 5.0 17.1 1.0

Iron binding site 4 out of 13 in 7w5e

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Iron binding site 4 out of 13 in the Oxidase Chap D49L Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Oxidase Chap D49L Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:12.2
occ:1.00
 OD2 B:ASP45 1.9 16.4 1.0
OE1 B:GLU4 2.0 14.7 1.0
O D:HOH312 2.2 12.4 1.0
OE2 B:GLU4 2.5 15.1 1.0
CD B:GLU4 2.6 13.7 1.0
CG B:ASP45 2.9 15.0 1.0
CB B:ASP45 3.3 11.9 1.0
O D:MET1 3.9 27.1 1.0
CE D:MET1 4.0 19.2 1.0
CG B:GLU4 4.0 8.9 1.0
OD1 B:ASP45 4.1 20.0 1.0
O B:HOH349 4.1 17.4 1.0
O B:HOH406 4.2 18.2 1.0
O B:HOH412 4.3 42.0 1.0
CD2 C:LEU67 4.3 10.0 1.0
C D:MET1 4.6 18.6 1.0
CB B:GLU4 4.7 12.3 1.0
O D:HOH382 4.7 42.5 1.0
CA B:ASP45 4.8 13.0 1.0
O B:ASP45 5.0 12.0 1.0

Iron binding site 5 out of 13 in 7w5e

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Iron binding site 5 out of 13 in the Oxidase Chap D49L Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Oxidase Chap D49L Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe202

b:16.1
occ:1.00
 OE1 B:GLU119 2.0 21.7 1.0
NE2 C:HIS7 2.1 16.8 1.0
NE2 B:HIS63 2.1 21.4 1.0
O B:HOH304 2.3 35.6 1.0
O A:HOH316 2.6 30.9 1.0
CD B:GLU119 2.8 26.0 1.0
OE2 B:GLU119 2.9 32.2 1.0
CE1 C:HIS7 3.0 20.6 1.0
CE1 B:HIS63 3.1 19.5 1.0
CD2 B:HIS63 3.1 20.3 1.0
CD2 C:HIS7 3.2 18.6 1.0
O B:HOH322 3.5 38.2 1.0
OH B:TYR109 3.7 36.3 1.0
CB B:ALA65 4.0 14.9 1.0
CE2 B:TYR109 4.0 22.6 1.0
ND1 C:HIS7 4.2 17.2 1.0
ND1 B:HIS63 4.2 20.8 1.0
CG B:GLU119 4.2 19.9 1.0
CG B:HIS63 4.2 17.2 1.0
CG C:HIS7 4.3 17.0 1.0
CZ B:TYR109 4.3 26.4 1.0
O A:HOH397 4.4 38.7 1.0
CB B:GLU119 4.6 16.2 1.0
CE1 A:TYR125 4.6 20.4 1.0
OH A:TYR125 4.9 29.5 1.0
OE1 B:GLN91 4.9 32.0 1.0

Iron binding site 6 out of 13 in 7w5e

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Iron binding site 6 out of 13 in the Oxidase Chap D49L Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Oxidase Chap D49L Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe203

b:16.5
occ:1.00
 NE2 B:HIS116 2.1 24.6 1.0
O B:HOH400 2.2 18.0 1.0
O B:HOH335 2.2 20.1 1.0
SG B:CYS64 2.3 18.3 1.0
CE1 B:HIS116 2.9 27.5 1.0
CD2 B:HIS116 3.1 27.2 1.0
CB B:CYS64 3.3 12.4 1.0
N B:CYS64 3.5 17.1 1.0
C B:HIS63 3.8 18.0 1.0
O B:HOH411 3.9 36.1 1.0
CA B:CYS64 3.9 13.8 1.0
OD2 B:ASP58 4.0 23.2 1.0
ND1 B:HIS116 4.1 27.2 1.0
O B:ASN117 4.1 17.1 1.0
O B:HIS63 4.1 18.1 1.0
O C:HOH315 4.1 18.6 1.0
O C:HOH357 4.2 24.8 1.0
CG B:HIS116 4.2 21.1 1.0
OG1 C:THR8 4.2 18.6 1.0
CG2 B:VAL10 4.3 16.5 1.0
CA B:HIS63 4.4 18.0 1.0
CG1 B:VAL10 4.4 21.3 1.0
CG B:ASP58 4.9 28.8 1.0
N B:HIS63 5.0 18.3 1.0

Iron binding site 7 out of 13 in 7w5e

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Iron binding site 7 out of 13 in the Oxidase Chap D49L Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Oxidase Chap D49L Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:10.8
occ:1.00
 OE1 C:GLU119 2.0 12.5 1.0
O C:HOH327 2.0 27.2 1.0
NE2 C:HIS63 2.1 15.7 1.0
NE2 B:HIS7 2.1 11.4 1.0
O B:HOH391 2.3 22.9 1.0
O C:HOH311 2.5 30.2 1.0
CD C:GLU119 2.9 14.0 1.0
CD2 C:HIS63 3.0 12.5 1.0
CE1 B:HIS7 3.0 14.5 1.0
CE1 C:HIS63 3.1 12.4 1.0
CD2 B:HIS7 3.1 13.9 1.0
OE2 C:GLU119 3.2 15.1 1.0
OH C:TYR109 4.0 15.7 1.0
CB C:ALA65 4.0 13.5 1.0
CG C:HIS63 4.2 12.8 1.0
ND1 C:HIS63 4.2 14.5 1.0
ND1 B:HIS7 4.2 11.5 1.0
O B:HOH405 4.2 35.4 1.0
CE2 C:TYR109 4.2 10.3 1.0
CG B:HIS7 4.2 12.2 1.0
O C:HOH385 4.3 36.0 1.0
CG C:GLU119 4.3 11.8 1.0
CB C:GLU119 4.6 10.2 1.0
CZ C:TYR109 4.6 16.0 1.0
OE1 C:GLN91 4.9 18.1 1.0
O C:HOH330 4.9 40.6 1.0
O C:HOH408 4.9 44.6 1.0
CD1 B:ILE9 4.9 14.2 1.0

Iron binding site 8 out of 13 in 7w5e

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Iron binding site 8 out of 13 in the Oxidase Chap D49L Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Oxidase Chap D49L Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe202

b:14.3
occ:1.00
 CE1 C:HIS116 2.0 18.0 1.0
O C:HOH358 2.2 20.8 1.0
O C:HOH321 2.2 17.6 1.0
NE2 C:HIS116 2.3 28.9 1.0
SG C:CYS64 2.3 16.9 1.0
ND1 C:HIS116 3.2 35.1 1.0
CB C:CYS64 3.3 13.9 1.0
N C:CYS64 3.5 9.9 1.0
CD2 C:HIS116 3.6 27.6 1.0
C C:HIS63 3.9 10.4 1.0
CG1 C:VAL10 3.9 18.1 1.0
CA C:CYS64 3.9 14.5 1.0
O C:ASN117 4.0 14.8 1.0
OD1 C:ASP58 4.0 18.1 1.0
CG C:HIS116 4.1 21.8 1.0
O C:HOH337 4.1 26.4 1.0
O B:HOH345 4.2 20.0 1.0
OG1 B:THR8 4.2 15.5 1.0
O C:HIS63 4.2 12.1 1.0
O B:HOH331 4.3 17.4 1.0
CG2 C:VAL10 4.5 20.0 1.0
CA C:HIS63 4.5 13.4 1.0
CG C:ASP58 4.6 26.1 1.0
CB C:VAL10 4.9 20.4 1.0
OD2 C:ASP58 4.9 33.7 1.0

Iron binding site 9 out of 13 in 7w5e

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Iron binding site 9 out of 13 in the Oxidase Chap D49L Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Oxidase Chap D49L Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe203

b:11.2
occ:1.00
 OD2 C:ASP45 2.0 14.3 1.0
OE1 C:GLU4 2.0 13.2 1.0
OD2 D:ASP45 2.0 19.3 1.0
OE1 D:GLU4 2.0 14.3 1.0
OE2 C:GLU4 2.5 18.1 1.0
OE2 D:GLU4 2.5 15.1 1.0
CD C:GLU4 2.6 14.2 1.0
CD D:GLU4 2.6 14.2 1.0
CG C:ASP45 3.1 14.7 1.0
CG D:ASP45 3.1 18.0 1.0
CB C:ASP45 3.6 13.2 1.0
CB D:ASP45 3.6 14.8 1.0
NH2 A:ARG123 3.9 17.6 1.0
CG C:GLU4 4.1 13.9 1.0
CG D:GLU4 4.1 14.3 1.0
OD1 C:ASP45 4.2 19.4 1.0
O D:HOH354 4.2 17.4 1.0
OD1 D:ASP45 4.2 16.2 1.0
O C:HOH356 4.2 13.7 1.0
CD2 A:LEU67 4.3 17.4 1.0
CD2 B:LEU67 4.3 13.8 1.0
CB C:GLU4 4.7 12.1 1.0
CB D:GLU4 4.8 15.8 1.0

Iron binding site 10 out of 13 in 7w5e

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Iron binding site 10 out of 13 in the Oxidase Chap D49L Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Oxidase Chap D49L Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe204

b:13.6
occ:1.00
 OE2 C:GLU111 1.8 42.1 1.0
ND1 C:HIS93 2.1 15.1 1.0
CD C:GLU111 2.6 21.4 1.0
OE1 C:GLU111 2.8 35.8 1.0
CE1 C:HIS93 3.0 12.8 1.0
CG C:HIS93 3.2 12.5 1.0
CB C:HIS93 3.5 13.1 1.0
CH2 C:TRP88 3.8 21.0 1.0
CG C:GLU111 3.9 28.4 1.0
CZ2 C:TRP88 4.0 14.8 1.0
NE2 C:HIS93 4.2 13.2 1.0
CD2 C:HIS93 4.2 12.0 1.0
CZ3 C:TRP88 4.2 20.6 1.0
CG1 C:VAL60 4.5 22.1 1.0
CE2 C:TRP88 4.6 15.4 1.0
OD1 C:ASN117 4.7 15.9 1.0
CE3 C:TRP88 4.8 15.6 1.0
CD2 C:TRP88 5.0 16.5 1.0

Reference:

Y.S.Wang, W.Zheng, N.Jiang, Y.X.Jin, Z.K.Meng, M.X.Sun, Y.L.Zong, T.Xu, J.Zhu, R.X.Tan. Alteration of the Catalytic Reaction Trajectory of A Vicinal Oxygen Chelate Enzyme By Directed Evolution. Angew.Chem.Int.Ed.Engl. V. 61 01321 2022.
ISSN: ESSN 1521-3773
PubMed: 35415958
DOI: 10.1002/ANIE.202201321
Page generated: Fri Aug 9 09:49:59 2024

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