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Manganese in PDB 7p9q: Crystal Structure of Indole 3-Carboxylic Acid Decarboxylase From Arthrobacter Nicotianae FI1612 in Complex with Co-Factor Prfmn.

Protein crystallography data

The structure of Crystal Structure of Indole 3-Carboxylic Acid Decarboxylase From Arthrobacter Nicotianae FI1612 in Complex with Co-Factor Prfmn., PDB code: 7p9q was solved by D.Gahloth, D.Leys, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.42 / 2.53
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 104.2, 195.45, 105.21, 90, 116.35, 90
R / Rfree (%) 18.4 / 22.1

Other elements in 7p9q:

The structure of Crystal Structure of Indole 3-Carboxylic Acid Decarboxylase From Arthrobacter Nicotianae FI1612 in Complex with Co-Factor Prfmn. also contains other interesting chemical elements:

Sodium (Na) 6 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Indole 3-Carboxylic Acid Decarboxylase From Arthrobacter Nicotianae FI1612 in Complex with Co-Factor Prfmn. (pdb code 7p9q). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Crystal Structure of Indole 3-Carboxylic Acid Decarboxylase From Arthrobacter Nicotianae FI1612 in Complex with Co-Factor Prfmn., PDB code: 7p9q:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 7p9q

Go back to Manganese Binding Sites List in 7p9q
Manganese binding site 1 out of 6 in the Crystal Structure of Indole 3-Carboxylic Acid Decarboxylase From Arthrobacter Nicotianae FI1612 in Complex with Co-Factor Prfmn.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Indole 3-Carboxylic Acid Decarboxylase From Arthrobacter Nicotianae FI1612 in Complex with Co-Factor Prfmn. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn502

b:93.7
occ:1.00
O2P A:4LU503 2.2 86.0 1.0
ND1 A:HIS173 2.3 90.0 1.0
OD1 A:ASN150 2.3 71.8 1.0
OE1 A:GLU217 2.3 84.4 1.0
O A:HOH652 2.4 75.6 1.0
O A:HOH603 2.5 105.0 1.0
CE1 A:HIS173 3.0 83.5 1.0
CD A:GLU217 3.2 74.0 1.0
P A:4LU503 3.3 88.7 1.0
CG A:HIS173 3.5 88.5 1.0
CG A:ASN150 3.5 75.7 1.0
O3P A:4LU503 3.5 71.2 1.0
OE2 A:GLU217 3.6 79.5 1.0
O A:ALA211 3.7 73.5 1.0
NA A:NA501 3.8 51.8 1.0
CB A:HIS173 3.9 87.2 1.0
O A:HOH671 4.0 48.2 1.0
ND2 A:ASN150 4.2 69.8 1.0
O A:PRO212 4.2 84.1 1.0
NE2 A:HIS173 4.3 81.6 1.0
O1P A:4LU503 4.3 83.4 1.0
O5' A:4LU503 4.4 93.2 1.0
CG A:GLU217 4.4 72.4 1.0
CD2 A:HIS173 4.5 81.3 1.0
CB A:ASN150 4.6 73.7 1.0
CB A:ALA211 4.6 84.0 1.0
O A:VAL215 4.7 80.1 1.0
O A:THR151 4.7 71.1 1.0
C A:ALA211 4.8 82.4 1.0
C A:PRO212 4.9 83.4 1.0

Manganese binding site 2 out of 6 in 7p9q

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Manganese binding site 2 out of 6 in the Crystal Structure of Indole 3-Carboxylic Acid Decarboxylase From Arthrobacter Nicotianae FI1612 in Complex with Co-Factor Prfmn.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Indole 3-Carboxylic Acid Decarboxylase From Arthrobacter Nicotianae FI1612 in Complex with Co-Factor Prfmn. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn502

b:92.5
occ:1.00
OD1 B:ASN150 2.3 67.5 1.0
OE1 B:GLU217 2.3 90.5 1.0
ND1 B:HIS173 2.4 101.3 1.0
O2P B:4LU503 2.4 87.5 1.0
O B:HOH633 2.5 90.8 1.0
CE1 B:HIS173 3.0 100.2 1.0
CD B:GLU217 3.1 84.9 1.0
OE2 B:GLU217 3.4 102.9 1.0
CG B:ASN150 3.5 71.7 1.0
P B:4LU503 3.5 89.8 1.0
O B:ALA211 3.5 78.6 1.0
CG B:HIS173 3.6 93.1 1.0
O3P B:4LU503 3.6 69.6 1.0
O B:HOH653 3.8 62.5 1.0
NA B:NA501 3.9 52.6 1.0
O B:PRO212 4.0 97.9 1.0
CB B:HIS173 4.1 92.0 1.0
ND2 B:ASN150 4.2 70.8 1.0
NE2 B:HIS173 4.3 92.0 1.0
CG B:GLU217 4.4 81.7 1.0
O1P B:4LU503 4.4 89.6 1.0
O B:VAL215 4.5 87.9 1.0
CB B:ALA211 4.5 80.6 1.0
CD2 B:HIS173 4.6 90.2 1.0
CB B:ASN150 4.6 71.2 1.0
C B:ALA211 4.6 84.8 1.0
O5' B:4LU503 4.7 100.1 1.0
C B:PRO212 4.7 92.6 1.0
O B:THR151 4.8 71.8 1.0
CA B:ASN150 5.0 71.0 1.0

Manganese binding site 3 out of 6 in 7p9q

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Manganese binding site 3 out of 6 in the Crystal Structure of Indole 3-Carboxylic Acid Decarboxylase From Arthrobacter Nicotianae FI1612 in Complex with Co-Factor Prfmn.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Indole 3-Carboxylic Acid Decarboxylase From Arthrobacter Nicotianae FI1612 in Complex with Co-Factor Prfmn. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn502

b:136.8
occ:1.00
OD1 C:ASN150 2.2 114.6 1.0
OE1 C:GLU217 2.2 134.1 1.0
ND1 C:HIS173 2.4 135.2 1.0
O2P C:4LU503 2.4 109.3 1.0
O C:HOH638 2.7 80.2 1.0
CD C:GLU217 3.0 120.7 1.0
CE1 C:HIS173 3.1 141.9 1.0
OE2 C:GLU217 3.3 117.8 1.0
CG C:ASN150 3.4 117.1 1.0
CG C:HIS173 3.5 132.2 1.0
P C:4LU503 3.5 124.5 1.0
O3P C:4LU503 3.7 119.5 1.0
O C:ALA211 3.7 133.2 1.0
O C:HOH619 3.9 76.1 1.0
CB C:HIS173 4.0 127.4 1.0
NA C:NA501 4.1 82.0 1.0
ND2 C:ASN150 4.1 119.0 1.0
O C:PRO212 4.2 136.9 1.0
CG C:GLU217 4.3 113.0 1.0
NE2 C:HIS173 4.3 147.5 1.0
CB C:ASN150 4.4 115.4 1.0
O C:VAL215 4.5 112.9 1.0
O1P C:4LU503 4.5 96.2 1.0
CD2 C:HIS173 4.6 143.1 1.0
CB C:ALA211 4.7 128.9 1.0
O5' C:4LU503 4.7 118.1 1.0
O C:THR151 4.7 104.6 1.0
C C:ALA211 4.8 132.6 1.0
CA C:ASN150 4.9 105.5 1.0
C C:PRO212 4.9 129.8 1.0
N C:THR151 5.0 104.6 1.0

Manganese binding site 4 out of 6 in 7p9q

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Manganese binding site 4 out of 6 in the Crystal Structure of Indole 3-Carboxylic Acid Decarboxylase From Arthrobacter Nicotianae FI1612 in Complex with Co-Factor Prfmn.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Indole 3-Carboxylic Acid Decarboxylase From Arthrobacter Nicotianae FI1612 in Complex with Co-Factor Prfmn. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn502

b:137.2
occ:1.00
OE1 D:GLU217 2.2 129.7 1.0
OD1 D:ASN150 2.5 109.7 1.0
ND1 D:HIS173 2.5 119.5 1.0
O2P D:4LU503 2.6 115.2 1.0
O D:HOH646 2.7 131.3 1.0
CD D:GLU217 2.9 121.8 1.0
CE1 D:HIS173 3.1 120.0 1.0
OE2 D:GLU217 3.3 132.0 1.0
O D:ALA211 3.4 126.0 1.0
O3P D:4LU503 3.4 121.7 1.0
P D:4LU503 3.6 121.7 1.0
CG D:ASN150 3.7 111.3 1.0
CG D:HIS173 3.8 109.8 1.0
O D:PRO212 3.9 135.1 1.0
O D:HOH614 4.0 80.2 1.0
NA D:NA501 4.1 78.7 1.0
CG D:GLU217 4.2 115.0 1.0
O D:VAL215 4.3 113.2 1.0
CB D:ALA211 4.3 131.5 1.0
CB D:HIS173 4.3 110.4 1.0
NE2 D:HIS173 4.4 114.8 1.0
C D:ALA211 4.4 126.9 1.0
ND2 D:ASN150 4.5 109.9 1.0
O5' D:4LU503 4.6 116.1 1.0
C D:PRO212 4.7 127.2 1.0
CD2 D:HIS173 4.7 111.8 1.0
CB D:ASN150 4.7 113.2 1.0
O1P D:4LU503 4.8 99.1 1.0
CB D:GLU217 4.8 108.9 1.0
O D:THR151 4.9 96.1 1.0

Manganese binding site 5 out of 6 in 7p9q

Go back to Manganese Binding Sites List in 7p9q
Manganese binding site 5 out of 6 in the Crystal Structure of Indole 3-Carboxylic Acid Decarboxylase From Arthrobacter Nicotianae FI1612 in Complex with Co-Factor Prfmn.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of Indole 3-Carboxylic Acid Decarboxylase From Arthrobacter Nicotianae FI1612 in Complex with Co-Factor Prfmn. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn502

b:135.3
occ:1.00
OE1 E:GLU217 2.0 129.8 1.0
O2P E:4LU503 2.2 129.6 1.0
OD1 E:ASN150 2.4 126.3 1.0
ND1 E:HIS173 2.7 121.9 1.0
CD E:GLU217 2.8 124.9 1.0
OE2 E:GLU217 3.2 131.0 1.0
CE1 E:HIS173 3.4 126.1 1.0
P E:4LU503 3.5 125.5 1.0
CG E:ASN150 3.6 127.5 1.0
O E:ALA211 3.6 129.5 1.0
O3P E:4LU503 3.7 138.1 1.0
NA E:NA501 3.8 84.8 1.0
CG E:HIS173 3.9 123.6 1.0
CG E:GLU217 4.1 118.5 1.0
O E:PRO212 4.2 131.0 1.0
O E:HOH624 4.2 92.8 1.0
ND2 E:ASN150 4.2 124.8 1.0
CB E:HIS173 4.3 128.8 1.0
CB E:ALA211 4.4 134.3 1.0
O5' E:4LU503 4.4 119.8 1.0
O E:THR151 4.5 128.2 1.0
O E:VAL215 4.5 130.3 1.0
O1P E:4LU503 4.6 102.7 1.0
C E:ALA211 4.6 135.7 1.0
NE2 E:HIS173 4.6 124.0 1.0
CB E:ASN150 4.6 125.3 1.0
CB E:GLU217 4.8 116.5 1.0
CD2 E:HIS173 4.9 123.2 1.0
N E:THR151 5.0 125.0 1.0
C E:PRO212 5.0 143.9 1.0
CA E:ASN150 5.0 124.1 1.0
O E:THR206 5.0 109.8 1.0

Manganese binding site 6 out of 6 in 7p9q

Go back to Manganese Binding Sites List in 7p9q
Manganese binding site 6 out of 6 in the Crystal Structure of Indole 3-Carboxylic Acid Decarboxylase From Arthrobacter Nicotianae FI1612 in Complex with Co-Factor Prfmn.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of Indole 3-Carboxylic Acid Decarboxylase From Arthrobacter Nicotianae FI1612 in Complex with Co-Factor Prfmn. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn502

b:140.8
occ:1.00
OE1 F:GLU217 2.0 163.0 1.0
O2P F:4LU503 2.4 128.6 1.0
OD1 F:ASN150 2.6 169.4 1.0
ND1 F:HIS173 2.7 135.1 1.0
CD F:GLU217 2.8 161.6 1.0
OE2 F:GLU217 3.2 173.8 1.0
CE1 F:HIS173 3.3 137.3 1.0
O F:ALA211 3.4 130.3 1.0
P F:4LU503 3.5 140.2 1.0
O3P F:4LU503 3.6 147.4 1.0
NA F:NA501 3.6 103.7 1.0
CG F:ASN150 3.8 158.3 1.0
CG F:HIS173 3.9 134.2 1.0
O F:PRO212 4.0 152.0 1.0
CG F:GLU217 4.1 149.0 1.0
CB F:ALA211 4.2 138.9 1.0
C F:ALA211 4.4 140.9 1.0
O F:VAL215 4.4 135.9 1.0
CB F:HIS173 4.4 136.9 1.0
ND2 F:ASN150 4.5 151.3 1.0
O1P F:4LU503 4.6 127.0 1.0
NE2 F:HIS173 4.6 132.0 1.0
O5' F:4LU503 4.6 131.0 1.0
CB F:GLU217 4.7 140.2 1.0
O F:THR151 4.7 132.7 1.0
C F:PRO212 4.8 156.3 1.0
CB F:ASN150 4.8 156.5 1.0
CD2 F:HIS173 4.9 131.2 1.0
CA F:ALA211 5.0 140.0 1.0

Reference:

D.Gahloth, K.Fisher, K.A.P.Payne, M.Cliff, C.Levy, D.Leys. Structural and Biochemical Characterization of the Prenylated Flavin Mononucleotide-Dependent Indole-3-Carboxylic Acid Decarboxylase. J.Biol.Chem. V. 298 01771 2022.
ISSN: ESSN 1083-351X
PubMed: 35218772
DOI: 10.1016/J.JBC.2022.101771
Page generated: Sun Oct 6 10:23:51 2024

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