Atomistry » Iron » PDB 3a0g-3ae5 » 3ae4
Atomistry »
  Iron »
    PDB 3a0g-3ae5 »
      3ae4 »

Iron in PDB 3ae4: Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with 2-Iodo-N-Methyl-Benzamide

Enzymatic activity of Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with 2-Iodo-N-Methyl-Benzamide

All present enzymatic activity of Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with 2-Iodo-N-Methyl-Benzamide:
1.3.5.1;

Protein crystallography data

The structure of Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with 2-Iodo-N-Methyl-Benzamide, PDB code: 3ae4 was solved by S.Harada, T.Sasaki, M.Shindo, Y.Kido, D.K.Inaoka, J.Omori, A.Osanai, K.Sakamoto, J.Mao, S.Matsuoka, M.Inoue, T.Honma, A.Tanaka, K.Kita, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.24 / 2.91
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 71.562, 84.222, 294.217, 90.00, 90.00, 90.00
R / Rfree (%) 22.2 / 25.7

Other elements in 3ae4:

The structure of Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with 2-Iodo-N-Methyl-Benzamide also contains other interesting chemical elements:

Iodine (I) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with 2-Iodo-N-Methyl-Benzamide (pdb code 3ae4). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 10 binding sites of Iron where determined in the Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with 2-Iodo-N-Methyl-Benzamide, PDB code: 3ae4:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 10 in 3ae4

Go back to Iron Binding Sites List in 3ae4
Iron binding site 1 out of 10 in the Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with 2-Iodo-N-Methyl-Benzamide


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 Porcine Heart Mitochondrial Complex II Bound with 2-Iodo-N-Methyl-Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:64.3
occ:1.00
 FE1 B:FES302 0.0 64.3 1.0
SG B:CYS65 2.0 65.6 1.0
S1 B:FES302 2.2 63.0 1.0
S2 B:FES302 2.2 61.5 1.0
SG B:CYS70 2.2 62.6 1.0
FE2 B:FES302 3.0 65.0 1.0
CB B:CYS65 3.2 66.6 1.0
N B:CYS65 3.3 66.6 1.0
CB B:CYS70 3.4 62.7 1.0
N B:CYS70 3.5 62.3 1.0
CA B:CYS65 3.7 67.5 1.0
N B:ARG66 3.8 69.3 1.0
CA B:CYS70 3.8 62.0 1.0
N B:GLY71 3.8 62.2 1.0
C B:CYS65 4.2 69.0 1.0
N B:SER72 4.2 63.9 1.0
C B:CYS70 4.3 61.6 1.0
N B:ILE69 4.3 64.3 1.0
N B:GLY68 4.3 67.2 1.0
SG B:CYS85 4.4 68.6 1.0
C B:SER64 4.4 66.9 1.0
N B:SER64 4.5 65.3 1.0
CB B:SER72 4.5 65.4 1.0
OG B:SER72 4.6 64.5 1.0
CA B:GLY68 4.7 65.9 1.0
C B:ILE69 4.7 62.2 1.0
N B:GLU67 4.7 70.1 1.0
CA B:ARG66 4.7 71.0 1.0
CA B:SER64 4.8 66.0 1.0
SG B:CYS73 4.8 69.8 1.0
CB B:SER64 4.9 64.9 1.0
CA B:GLY71 4.9 62.2 1.0
C B:GLY68 4.9 64.7 1.0
CA B:SER72 5.0 64.8 1.0

Iron binding site 2 out of 10 in 3ae4

Go back to Iron Binding Sites List in 3ae4
Iron binding site 2 out of 10 in the Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with 2-Iodo-N-Methyl-Benzamide


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 Porcine Heart Mitochondrial Complex II Bound with 2-Iodo-N-Methyl-Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:65.0
occ:1.00
 FE2 B:FES302 0.0 65.0 1.0
SG B:CYS73 2.1 69.8 1.0
S2 B:FES302 2.2 61.5 1.0
S1 B:FES302 2.2 63.0 1.0
SG B:CYS85 2.6 68.6 1.0
FE1 B:FES302 3.0 64.3 1.0
CB B:CYS73 3.4 68.6 1.0
CB B:CYS85 3.5 70.5 1.0
N B:CYS73 3.7 66.7 1.0
CA B:CYS73 4.2 68.0 1.0
CB B:LEU83 4.2 65.8 1.0
N B:CYS85 4.3 70.7 1.0
N B:SER72 4.4 63.9 1.0
SG B:CYS65 4.4 65.6 1.0
CD2 B:LEU83 4.5 63.5 1.0
CA B:CYS85 4.5 71.8 1.0
CA B:GLY68 4.5 65.9 1.0
N B:GLY68 4.6 67.2 1.0
CD1 B:LEU83 4.6 63.7 1.0
CG B:LEU83 4.7 64.0 1.0
N B:ARG66 4.8 69.3 1.0
C B:SER72 4.8 65.9 1.0
SG B:CYS70 4.8 62.6 1.0
N B:GLY71 4.9 62.2 1.0
CA B:ARG66 5.0 71.0 1.0
CA B:SER72 5.0 64.8 1.0
CA B:LEU83 5.0 66.4 1.0

Iron binding site 3 out of 10 in 3ae4

Go back to Iron Binding Sites List in 3ae4
Iron binding site 3 out of 10 in the Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with 2-Iodo-N-Methyl-Benzamide


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 Porcine Heart Mitochondrial Complex II Bound with 2-Iodo-N-Methyl-Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe303

b:59.3
occ:1.00
 FE1 B:SF4303 0.0 59.3 1.0
S4 B:SF4303 2.3 59.3 1.0
S2 B:SF4303 2.3 59.5 1.0
S3 B:SF4303 2.3 59.1 1.0
SG B:CYS158 2.4 56.2 1.0
FE3 B:SF4303 2.6 59.9 1.0
FE2 B:SF4303 2.7 60.2 1.0
FE4 B:SF4303 2.7 59.7 1.0
CB B:CYS158 3.4 56.6 1.0
N B:ILE159 3.7 57.8 1.0
CA B:CYS158 3.8 57.5 1.0
S1 B:SF4303 3.9 60.5 1.0
N B:LEU160 4.1 56.9 1.0
C B:CYS158 4.3 57.4 1.0
CD1 B:LEU229 4.3 60.1 1.0
CA B:LEU160 4.7 56.6 1.0
CA B:ILE159 4.8 57.9 1.0
N B:CYS161 4.9 58.7 1.0
SG B:CYS164 4.9 55.6 1.0
SG B:CYS161 4.9 61.9 1.0
C B:ILE159 4.9 57.6 1.0

Iron binding site 4 out of 10 in 3ae4

Go back to Iron Binding Sites List in 3ae4
Iron binding site 4 out of 10 in the Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with 2-Iodo-N-Methyl-Benzamide


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 Porcine Heart Mitochondrial Complex II Bound with 2-Iodo-N-Methyl-Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe303

b:60.2
occ:1.00
 FE2 B:SF4303 0.0 60.2 1.0
S3 B:SF4303 2.3 59.1 1.0
S4 B:SF4303 2.3 59.3 1.0
S1 B:SF4303 2.3 60.5 1.0
SG B:CYS225 2.5 62.9 1.0
FE4 B:SF4303 2.7 59.7 1.0
FE1 B:SF4303 2.7 59.3 1.0
FE3 B:SF4303 2.7 59.9 1.0
CB B:CYS225 3.7 64.1 1.0
S2 B:SF4303 3.9 59.5 1.0
CD B:PRO226 3.9 65.1 1.0
CA B:CYS225 4.2 65.2 1.0
CD1 B:LEU229 4.2 60.1 1.0
CB B:LEU229 4.5 61.8 1.0
CG B:LEU229 4.5 62.0 1.0
CG B:PRO226 4.6 65.7 1.0
N B:PRO226 4.6 67.0 1.0
SG B:CYS161 4.6 61.9 1.0
CB B:LYS227 4.6 64.0 1.0
CG B:LYS227 4.7 63.2 1.0
SG B:CYS164 4.7 55.6 1.0
N B:LYS227 4.8 66.5 1.0
C B:CYS225 4.8 67.2 1.0

Iron binding site 5 out of 10 in 3ae4

Go back to Iron Binding Sites List in 3ae4
Iron binding site 5 out of 10 in the Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with 2-Iodo-N-Methyl-Benzamide


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 Porcine Heart Mitochondrial Complex II Bound with 2-Iodo-N-Methyl-Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe303

b:59.9
occ:1.00
 FE3 B:SF4303 0.0 59.9 1.0
S2 B:SF4303 2.3 59.5 1.0
S4 B:SF4303 2.3 59.3 1.0
S1 B:SF4303 2.3 60.5 1.0
SG B:CYS164 2.3 55.6 1.0
FE1 B:SF4303 2.6 59.3 1.0
FE4 B:SF4303 2.7 59.7 1.0
FE2 B:SF4303 2.7 60.2 1.0
CB B:CYS164 3.5 57.1 1.0
S3 B:SF4303 3.9 59.1 1.0
CB B:ALA182 4.1 57.0 1.0
N B:CYS164 4.2 58.8 1.0
CA B:ALA182 4.3 56.9 1.0
CA B:CYS164 4.5 58.0 1.0
CG B:PRO231 4.6 59.8 1.0
SG B:CYS158 4.7 56.2 1.0
SG B:CYS161 4.7 61.9 1.0
N B:ALA182 4.8 57.1 1.0
SG B:CYS225 4.9 62.9 1.0

Iron binding site 6 out of 10 in 3ae4

Go back to Iron Binding Sites List in 3ae4
Iron binding site 6 out of 10 in the Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with 2-Iodo-N-Methyl-Benzamide


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 Porcine Heart Mitochondrial Complex II Bound with 2-Iodo-N-Methyl-Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe303

b:59.7
occ:1.00
 FE4 B:SF4303 0.0 59.7 1.0
SG B:CYS161 2.3 61.9 1.0
S1 B:SF4303 2.3 60.5 1.0
S3 B:SF4303 2.3 59.1 1.0
S2 B:SF4303 2.3 59.5 1.0
FE2 B:SF4303 2.7 60.2 1.0
FE3 B:SF4303 2.7 59.9 1.0
FE1 B:SF4303 2.7 59.3 1.0
CB B:CYS161 3.7 61.4 1.0
N B:CYS161 3.7 58.7 1.0
S4 B:SF4303 3.9 59.3 1.0
N B:ALA162 4.0 59.0 1.0
CD B:PRO226 4.1 65.1 1.0
CA B:CYS161 4.1 60.2 1.0
N B:CYS163 4.3 60.3 1.0
CG B:PRO226 4.3 65.7 1.0
C B:CYS161 4.4 60.3 1.0
CB B:CYS163 4.6 62.2 1.0
SG B:CYS164 4.6 55.6 1.0
N B:LEU160 4.7 56.9 1.0
C B:LEU160 4.8 57.8 1.0
SG B:CYS158 4.8 56.2 1.0
SG B:CYS225 4.9 62.9 1.0
N B:CYS164 4.9 58.8 1.0
CG2 B:ILE159 4.9 60.2 1.0
CA B:ALA162 4.9 59.0 1.0
CA B:LEU160 5.0 56.6 1.0
N B:ILE159 5.0 57.8 1.0

Iron binding site 7 out of 10 in 3ae4

Go back to Iron Binding Sites List in 3ae4
Iron binding site 7 out of 10 in the Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with 2-Iodo-N-Methyl-Benzamide


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 Porcine Heart Mitochondrial Complex II Bound with 2-Iodo-N-Methyl-Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe304

b:67.9
occ:1.00
 FE1 B:F3S304 0.0 67.9 1.0
S3 B:F3S304 2.2 67.0 1.0
S1 B:F3S304 2.2 66.2 1.0
S2 B:F3S304 2.2 70.5 1.0
SG B:CYS221 2.2 58.0 1.0
FE4 B:F3S304 2.4 70.4 1.0
FE3 B:F3S304 2.8 68.3 1.0
CB B:CYS221 3.4 58.2 1.0
N B:CYS221 4.0 60.4 1.0
N B:MET219 4.0 61.3 1.0
SG B:CYS215 4.2 53.6 1.0
S4 B:F3S304 4.2 70.2 1.0
CA B:MET219 4.2 61.8 1.0
CA B:CYS221 4.3 59.8 1.0
N B:ASN220 4.5 62.1 1.0
CB B:PRO181 4.5 58.0 1.0
SG B:CYS168 4.6 57.2 1.0
C B:MET219 4.6 62.5 1.0
CG B:PRO181 4.7 58.3 1.0
CA B:GLY232 4.8 61.2 1.0
N B:GLY232 4.9 60.5 1.0

Iron binding site 8 out of 10 in 3ae4

Go back to Iron Binding Sites List in 3ae4
Iron binding site 8 out of 10 in the Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with 2-Iodo-N-Methyl-Benzamide


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 Porcine Heart Mitochondrial Complex II Bound with 2-Iodo-N-Methyl-Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe304

b:68.3
occ:1.00
 FE3 B:F3S304 0.0 68.3 1.0
SG B:CYS168 2.0 57.2 1.0
S3 B:F3S304 2.2 67.0 1.0
S4 B:F3S304 2.2 70.2 1.0
S1 B:F3S304 2.2 66.2 1.0
FE4 B:F3S304 2.2 70.4 1.0
FE1 B:F3S304 2.8 67.9 1.0
CB B:CYS168 3.1 57.6 1.0
CA B:CYS168 4.0 59.0 1.0
S2 B:F3S304 4.1 70.5 1.0
SG B:CYS215 4.2 53.6 1.0
OH B:TYR178 4.4 55.4 1.0
CB B:SER170 4.7 57.5 1.0
C B:CYS168 4.7 59.6 1.0
CE2 B:TYR178 4.8 56.0 1.0
CB B:ILE218 4.8 61.1 1.0
CD B:PRO169 4.8 61.1 1.0
SG B:CYS221 4.8 58.0 1.0
CD B:PRO181 4.9 58.2 1.0
N B:PRO169 4.9 60.4 1.0
N B:SER170 4.9 59.1 1.0

Iron binding site 9 out of 10 in 3ae4

Go back to Iron Binding Sites List in 3ae4
Iron binding site 9 out of 10 in the Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with 2-Iodo-N-Methyl-Benzamide


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with 2-Iodo-N-Methyl-Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe304

b:70.4
occ:1.00
 FE4 B:F3S304 0.0 70.4 1.0
S4 B:F3S304 2.2 70.2 1.0
S2 B:F3S304 2.2 70.5 1.0
S3 B:F3S304 2.2 67.0 1.0
FE3 B:F3S304 2.2 68.3 1.0
SG B:CYS215 2.4 53.6 1.0
FE1 B:F3S304 2.4 67.9 1.0
S1 B:F3S304 3.0 66.2 1.0
CB B:CYS215 3.8 56.0 1.0
N B:ILE218 3.9 60.5 1.0
N B:THR217 4.1 59.2 1.0
SG B:CYS168 4.1 57.2 1.0
CA B:CYS215 4.2 56.3 1.0
CA B:THR217 4.2 60.0 1.0
N B:MET219 4.3 61.3 1.0
OH B:TYR178 4.5 55.4 1.0
N B:HIS216 4.5 58.0 1.0
C B:THR217 4.6 60.8 1.0
SG B:CYS221 4.6 58.0 1.0
CB B:ILE218 4.7 61.1 1.0
CA B:ILE218 4.7 61.4 1.0
C B:CYS215 4.8 57.3 1.0

Iron binding site 10 out of 10 in 3ae4

Go back to Iron Binding Sites List in 3ae4
Iron binding site 10 out of 10 in the Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with 2-Iodo-N-Methyl-Benzamide


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with 2-Iodo-N-Methyl-Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe1305

b:64.4
occ:1.00
 FE C:HEM1305 0.0 64.4 1.0
NC C:HEM1305 1.9 63.1 1.0
ND C:HEM1305 2.1 63.4 1.0
NA C:HEM1305 2.1 63.7 1.0
NB C:HEM1305 2.1 63.9 1.0
NE2 C:HIS101 2.2 63.1 1.0
NE2 D:HIS79 2.2 62.6 1.0
C4C C:HEM1305 3.0 63.6 1.0
C1C C:HEM1305 3.0 63.8 1.0
C1D C:HEM1305 3.0 63.7 1.0
CD2 C:HIS101 3.1 61.5 1.0
C4B C:HEM1305 3.1 64.0 1.0
C4D C:HEM1305 3.1 63.6 1.0
C1A C:HEM1305 3.1 64.7 1.0
C4A C:HEM1305 3.1 64.5 1.0
CD2 D:HIS79 3.1 62.5 1.0
C1B C:HEM1305 3.1 64.1 1.0
CE1 D:HIS79 3.2 61.2 1.0
CE1 C:HIS101 3.2 63.2 1.0
CHD C:HEM1305 3.3 63.8 1.0
CHC C:HEM1305 3.4 63.7 1.0
CHA C:HEM1305 3.4 64.2 1.0
CHB C:HEM1305 3.5 64.5 1.0
C3C C:HEM1305 4.2 64.2 1.0
C2C C:HEM1305 4.2 63.9 1.0
CG C:HIS101 4.2 61.4 1.0
ND1 C:HIS101 4.3 62.2 1.0
ND1 D:HIS79 4.3 61.1 1.0
C2D C:HEM1305 4.3 63.6 1.0
CG D:HIS79 4.3 61.1 1.0
C2A C:HEM1305 4.3 65.8 1.0
C3D C:HEM1305 4.3 63.8 1.0
C3B C:HEM1305 4.3 64.4 1.0
C3A C:HEM1305 4.3 65.1 1.0
C2B C:HEM1305 4.4 64.2 1.0
NE2 C:HIS45 4.8 66.3 1.0

Reference:

S.Harada, T.Sasaki, M.Shindo, Y.Kido, D.K.Inaoka, J.Omori, A.Osanai, K.Sakamoto, J.Mao, S.Matsuoka, M.Inoue, T.Honma, A.Tanaka, K.Kita. Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with 2-Iodo-N-Methyl-Benzamide To Be Published.
Page generated: Sun Aug 4 06:47:38 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy