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Manganese in PDB 4efd: Crystal Structure of An M17 Aminopeptidase From Trypanosoma Brucei, TB427TMP.02.4440

Protein crystallography data

The structure of Crystal Structure of An M17 Aminopeptidase From Trypanosoma Brucei, TB427TMP.02.4440, PDB code: 4efd was solved by A.K.Wernimont, K.T.Osman, P.Loppnau, C.H.Arrowsmith, A.M.Edwards, C.Bountra, R.Hui, Y.H.Lin, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.45
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 161.916, 161.740, 176.315, 90.00, 90.00, 90.00
R / Rfree (%) 22.7 / 25.3

Other elements in 4efd:

The structure of Crystal Structure of An M17 Aminopeptidase From Trypanosoma Brucei, TB427TMP.02.4440 also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of An M17 Aminopeptidase From Trypanosoma Brucei, TB427TMP.02.4440 (pdb code 4efd). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Crystal Structure of An M17 Aminopeptidase From Trypanosoma Brucei, TB427TMP.02.4440, PDB code: 4efd:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 4efd

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Manganese binding site 1 out of 8 in the Crystal Structure of An M17 Aminopeptidase From Trypanosoma Brucei, TB427TMP.02.4440


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 An M17 Aminopeptidase From Trypanosoma Brucei, TB427TMP.02.4440 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn603

b:95.3
occ:1.00
 O A:HOH794 3.0 51.0 1.0
NH1 D:ARG466 3.8 49.9 1.0
CE1 A:HIS413 4.0 42.4 1.0
NE2 A:HIS413 4.1 42.4 1.0
NH2 D:ARG466 4.2 49.8 1.0
CZ D:ARG466 4.5 49.7 1.0
CB A:ARG412 4.8 40.5 1.0
CB A:ASN502 5.0 35.8 1.0

Manganese binding site 2 out of 8 in 4efd

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Manganese binding site 2 out of 8 in the Crystal Structure of An M17 Aminopeptidase From Trypanosoma Brucei, TB427TMP.02.4440


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 An M17 Aminopeptidase From Trypanosoma Brucei, TB427TMP.02.4440 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn603

b:92.1
occ:1.00
 O B:HOH828 2.8 41.7 1.0
NH1 E:ARG466 3.9 38.9 1.0
NH2 E:ARG466 4.0 38.7 1.0
O B:HOH751 4.1 52.6 1.0
NE2 B:HIS413 4.3 37.6 1.0
CZ E:ARG466 4.5 38.7 1.0
CE1 B:HIS413 4.5 37.7 1.0
CB B:ASN502 4.9 34.3 1.0

Manganese binding site 3 out of 8 in 4efd

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Manganese binding site 3 out of 8 in the Crystal Structure of An M17 Aminopeptidase From Trypanosoma Brucei, TB427TMP.02.4440


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 An M17 Aminopeptidase From Trypanosoma Brucei, TB427TMP.02.4440 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn604

b:80.4
occ:1.00
 O E:HOH859 3.0 41.3 1.0
NH1 B:ARG466 3.9 42.5 1.0
NH2 B:ARG466 3.9 42.3 1.0
CE1 E:HIS413 4.0 33.9 1.0
O E:HOH825 4.0 46.4 1.0
NE2 E:HIS413 4.1 33.8 1.0
CZ B:ARG466 4.4 42.3 1.0
CB E:ASN502 4.9 34.4 1.0

Manganese binding site 4 out of 8 in 4efd

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Manganese binding site 4 out of 8 in the Crystal Structure of An M17 Aminopeptidase From Trypanosoma Brucei, TB427TMP.02.4440


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 An M17 Aminopeptidase From Trypanosoma Brucei, TB427TMP.02.4440 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn604

b:82.9
occ:1.00
 O F:HOH812 2.2 42.3 1.0
MN F:MN603 3.1 85.8 1.0
NH2 C:ARG466 3.6 41.4 1.0
NH1 C:ARG466 3.8 41.9 1.0
CE1 F:HIS413 3.9 34.6 1.0
NE2 F:HIS413 4.1 34.5 1.0
CZ C:ARG466 4.2 41.4 1.0
O F:HOH814 4.6 47.2 1.0
O F:HOH808 4.7 50.3 1.0

Manganese binding site 5 out of 8 in 4efd

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Manganese binding site 5 out of 8 in the Crystal Structure of An M17 Aminopeptidase From Trypanosoma Brucei, TB427TMP.02.4440


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 An M17 Aminopeptidase From Trypanosoma Brucei, TB427TMP.02.4440 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn605

b:0.4
occ:1.00
 MN F:MN604 2.6 100.0 1.0
OG C:SER503 3.8 37.5 1.0
N C:SER503 4.0 36.9 1.0
NH1 F:ARG466 4.0 41.9 1.0
CB C:SER503 4.1 37.3 1.0
CB C:ASN502 4.3 36.3 1.0
CA C:SER503 4.7 37.2 1.0
CA C:ASN502 4.7 36.2 1.0
C C:ASN502 4.8 36.5 1.0

Manganese binding site 6 out of 8 in 4efd

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Manganese binding site 6 out of 8 in the Crystal Structure of An M17 Aminopeptidase From Trypanosoma Brucei, TB427TMP.02.4440


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 An M17 Aminopeptidase From Trypanosoma Brucei, TB427TMP.02.4440 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn603

b:94.2
occ:1.00
 O D:HOH795 2.3 44.4 1.0
O D:HOH787 3.0 43.1 1.0
O D:HOH794 3.1 41.6 1.0
CE1 D:HIS413 3.9 42.6 1.0
NH1 A:ARG466 3.9 45.3 1.0
NE2 D:HIS413 4.0 42.6 1.0
NH2 A:ARG466 4.0 45.1 1.0
CZ A:ARG466 4.4 45.0 1.0
CB D:ARG412 4.8 41.4 1.0
ND1 D:HIS413 4.9 42.7 1.0
O D:HOH736 4.9 47.5 1.0

Manganese binding site 7 out of 8 in 4efd

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Manganese binding site 7 out of 8 in the Crystal Structure of An M17 Aminopeptidase From Trypanosoma Brucei, TB427TMP.02.4440


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Crystal Structure of An M17 Aminopeptidase From Trypanosoma Brucei, TB427TMP.02.4440 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn603

b:85.8
occ:1.00
 O F:HOH808 2.6 50.3 1.0
MN C:MN604 3.1 82.9 1.0
N F:SER503 3.4 33.3 1.0
O F:HOH812 3.6 42.3 1.0
OG F:SER503 3.6 33.5 1.0
CB F:SER503 3.8 33.1 1.0
CB F:ASN502 3.8 33.8 1.0
CA F:SER503 4.2 33.1 1.0
CA F:ASN502 4.2 33.9 1.0
C F:ASN502 4.2 33.6 1.0
NH1 C:ARG466 4.3 41.9 1.0
CG F:ASN502 4.8 33.7 1.0
O F:HOH814 4.9 47.2 1.0

Manganese binding site 8 out of 8 in 4efd

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Manganese binding site 8 out of 8 in the Crystal Structure of An M17 Aminopeptidase From Trypanosoma Brucei, TB427TMP.02.4440


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Crystal Structure of An M17 Aminopeptidase From Trypanosoma Brucei, TB427TMP.02.4440 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn604

b:100.0
occ:1.00
 MN C:MN605 2.6 0.4 1.0
NH2 F:ARG466 3.8 41.9 1.0
NE2 C:HIS413 3.9 37.9 1.0
NH1 F:ARG466 3.9 41.9 1.0
CE1 C:HIS413 4.0 37.9 1.0
CZ F:ARG466 4.4 41.8 1.0

Reference:

A.K.Wernimont, K.T.Osman, P.Loppnau, C.H.Arrowsmith, A.M.Edwards, C.Bountra, R.Hui, Y.H.Lin. Crystal Structure of An M17 Aminopeptidase From Trypanosoma Brucei, TB427TMP.02.4440 To Be Published.
Page generated: Sat Aug 16 13:55:26 2025

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