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Manganese in PDB 4ggf: Crystal Structure of MN2+ Bound Calprotectin

Protein crystallography data

The structure of Crystal Structure of MN2+ Bound Calprotectin, PDB code: 4ggf was solved by S.M.Damo, G.Fritz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.64 / 1.60
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 82.027, 217.002, 53.022, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 20.2

Other elements in 4ggf:

The structure of Crystal Structure of MN2+ Bound Calprotectin also contains other interesting chemical elements:

Calcium (Ca) 12 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of MN2+ Bound Calprotectin (pdb code 4ggf). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 7 binding sites of Manganese where determined in the Crystal Structure of MN2+ Bound Calprotectin, PDB code: 4ggf:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7;

Manganese binding site 1 out of 7 in 4ggf

Go back to Manganese Binding Sites List in 4ggf
Manganese binding site 1 out of 7 in the Crystal Structure of MN2+ Bound Calprotectin


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 MN2+ Bound Calprotectin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn201

b:20.0
occ:1.00
 NE2 C:HIS103 2.2 22.5 1.0
NE2 C:HIS95 2.3 20.7 1.0
NE2 A:HIS17 2.3 18.6 1.0
NE2 C:HIS91 2.3 19.9 1.0
NE2 C:HIS105 2.3 20.8 1.0
NE2 A:HIS27 2.4 19.8 1.0
CD2 C:HIS103 3.2 23.8 1.0
CE1 A:HIS17 3.2 18.5 1.0
CE1 C:HIS103 3.2 23.6 1.0
CD2 C:HIS105 3.2 22.7 1.0
CE1 C:HIS95 3.2 21.8 1.0
CE1 C:HIS91 3.2 20.0 1.0
CD2 C:HIS95 3.3 20.7 1.0
CD2 A:HIS27 3.3 19.4 1.0
CD2 A:HIS17 3.3 18.9 1.0
CD2 C:HIS91 3.3 19.9 1.0
CE1 A:HIS27 3.3 20.9 1.0
CE1 C:HIS105 3.4 20.6 1.0
ND1 A:HIS17 4.3 17.9 1.0
ND1 C:HIS103 4.4 24.9 1.0
CG C:HIS103 4.4 25.1 1.0
ND1 C:HIS95 4.4 22.3 1.0
CG A:HIS17 4.4 19.0 1.0
CG C:HIS105 4.4 23.0 1.0
ND1 C:HIS91 4.4 19.5 1.0
CG C:HIS95 4.4 20.9 1.0
ND1 C:HIS105 4.5 21.9 1.0
CG A:HIS27 4.5 19.4 1.0
ND1 A:HIS27 4.5 19.8 1.0
CG C:HIS91 4.5 18.7 1.0

Manganese binding site 2 out of 7 in 4ggf

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Manganese binding site 2 out of 7 in the Crystal Structure of MN2+ Bound Calprotectin


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 MN2+ Bound Calprotectin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn202

b:17.8
occ:0.40
 OD1 C:ASP30 1.7 20.6 0.5
OD1 C:ASP30 1.7 22.9 0.5
NE2 A:HIS87 1.9 20.5 1.0
NE2 A:HIS83 2.1 16.4 1.0
NE2 C:HIS20 2.2 17.4 1.0
CG C:ASP30 2.3 21.0 0.5
OD2 C:ASP30 2.4 21.5 0.5
CG C:ASP30 2.7 21.8 0.5
CD2 A:HIS87 2.8 18.7 1.0
CE1 A:HIS87 3.0 20.8 1.0
CD2 A:HIS83 3.0 16.7 1.0
O C:HOH380 3.0 36.4 1.0
CE1 A:HIS83 3.1 16.8 1.0
CD2 C:HIS20 3.1 16.2 1.0
OD2 C:ASP30 3.2 23.6 0.5
CE1 C:HIS20 3.3 17.2 1.0
CB C:ASP30 3.7 21.5 0.5
CB C:ASP30 3.9 22.4 0.5
CG A:HIS87 4.0 19.4 1.0
ND1 A:HIS87 4.1 19.6 1.0
CG A:HIS83 4.1 16.0 1.0
ND1 A:HIS83 4.2 16.7 1.0
CG C:HIS20 4.3 15.9 1.0
ND1 C:HIS20 4.4 16.0 1.0
CA C:ASP30 4.4 20.8 0.5
CA C:ASP30 4.4 20.3 0.5
CE1 C:PHE19 4.5 16.6 1.0
OG A:SER86 4.6 17.7 1.0
O C:ASP30 4.8 19.6 0.5
O A:HIS83 4.8 16.9 1.0
O C:ASP30 4.9 19.4 0.5
O C:HOH332 4.9 21.5 1.0
CD1 C:PHE19 4.9 15.5 1.0

Manganese binding site 3 out of 7 in 4ggf

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Manganese binding site 3 out of 7 in the Crystal Structure of MN2+ Bound Calprotectin


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 MN2+ Bound Calprotectin within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mn201

b:19.4
occ:0.50
 OD1 L:ASP30 1.6 25.9 0.5
NE2 K:HIS87 2.0 23.9 1.0
NE2 K:HIS83 2.1 21.2 1.0
OD1 L:ASP30 2.1 27.5 0.5
OD2 L:ASP30 2.2 28.5 0.5
CG L:ASP30 2.3 26.0 0.5
CG L:ASP30 2.3 27.7 0.5
NE2 L:HIS20 2.3 19.6 1.0
OD2 L:ASP30 2.6 26.6 0.5
O L:HOH357 2.7 36.1 1.0
CD2 K:HIS87 2.9 24.0 1.0
CE1 K:HIS87 3.0 24.0 1.0
CE1 K:HIS83 3.1 21.8 1.0
CD2 K:HIS83 3.1 20.3 1.0
CD2 L:HIS20 3.2 18.9 1.0
CE1 L:HIS20 3.3 19.3 1.0
CB L:ASP30 3.6 27.8 0.5
CB L:ASP30 3.7 26.5 0.5
CG K:HIS87 4.1 25.4 1.0
ND1 K:HIS87 4.1 25.1 1.0
ND1 K:HIS83 4.2 21.2 1.0
CG K:HIS83 4.2 19.5 1.0
CA L:ASP30 4.4 25.3 0.5
CA L:ASP30 4.4 24.5 0.5
ND1 L:HIS20 4.4 18.4 1.0
CG L:HIS20 4.5 17.7 1.0
O L:HOH307 4.5 22.5 1.0
O L:ASP30 4.6 22.8 0.5
O L:ASP30 4.6 23.1 0.5
CE2 L:PHE19 4.6 17.8 1.0
OG K:SER86 4.9 22.9 1.0
CD2 L:PHE19 5.0 16.7 1.0

Manganese binding site 4 out of 7 in 4ggf

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Manganese binding site 4 out of 7 in the Crystal Structure of MN2+ Bound Calprotectin


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 MN2+ Bound Calprotectin within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mn202

b:17.5
occ:1.00
 NE2 L:HIS91 2.2 15.5 1.0
NE2 K:HIS27 2.3 19.1 1.0
NE2 K:HIS17 2.3 16.5 1.0
NE2 L:HIS103 2.3 20.9 1.0
NE2 L:HIS95 2.3 20.0 1.0
NE2 L:HIS105 2.4 18.5 1.0
CE1 L:HIS91 3.1 16.9 1.0
CE1 K:HIS17 3.2 15.6 1.0
CD2 K:HIS27 3.2 18.2 1.0
CD2 L:HIS105 3.2 19.8 1.0
CD2 L:HIS91 3.2 15.3 1.0
CD2 L:HIS103 3.2 23.9 1.0
CD2 K:HIS17 3.3 16.2 1.0
CD2 L:HIS95 3.3 19.2 1.0
CE1 K:HIS27 3.3 20.7 1.0
CE1 L:HIS95 3.3 22.0 1.0
CE1 L:HIS103 3.3 22.5 1.0
CE1 L:HIS105 3.4 18.7 1.0
ND1 L:HIS91 4.3 15.9 1.0
ND1 K:HIS17 4.3 15.2 1.0
CG L:HIS91 4.4 15.0 1.0
CG K:HIS27 4.4 17.5 1.0
CG K:HIS17 4.4 16.1 1.0
ND1 K:HIS27 4.4 19.7 1.0
ND1 L:HIS103 4.4 26.2 1.0
CG L:HIS103 4.4 26.4 1.0
ND1 L:HIS95 4.4 21.6 1.0
CG L:HIS105 4.4 20.3 1.0
CG L:HIS95 4.5 20.6 1.0
ND1 L:HIS105 4.5 20.0 1.0

Manganese binding site 5 out of 7 in 4ggf

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Manganese binding site 5 out of 7 in the Crystal Structure of MN2+ Bound Calprotectin


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 MN2+ Bound Calprotectin within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mn201

b:13.8
occ:1.00
 NE2 S:HIS27 2.3 15.1 1.0
NE2 T:HIS95 2.3 16.0 1.0
NE2 T:HIS91 2.3 14.9 1.0
NE2 T:HIS105 2.3 15.8 1.0
NE2 T:HIS103 2.3 15.5 1.0
NE2 S:HIS17 2.3 13.0 1.0
CD2 T:HIS105 3.2 16.2 1.0
CE1 S:HIS27 3.2 16.1 1.0
CE1 S:HIS17 3.2 12.2 1.0
CD2 T:HIS91 3.2 14.7 1.0
CD2 S:HIS27 3.2 14.0 1.0
CD2 T:HIS95 3.2 16.3 1.0
CE1 T:HIS95 3.2 16.7 1.0
CE1 T:HIS91 3.3 15.3 1.0
CE1 T:HIS103 3.3 15.9 1.0
CD2 S:HIS17 3.3 12.7 1.0
CE1 T:HIS105 3.3 16.1 1.0
CD2 T:HIS103 3.3 16.1 1.0
ND1 S:HIS17 4.3 12.5 1.0
ND1 S:HIS27 4.4 15.6 1.0
ND1 T:HIS95 4.4 17.0 1.0
CG S:HIS17 4.4 12.8 1.0
CG S:HIS27 4.4 14.4 1.0
CG T:HIS95 4.4 17.3 1.0
CG T:HIS105 4.4 16.4 1.0
ND1 T:HIS91 4.4 15.1 1.0
CG T:HIS91 4.4 14.8 1.0
ND1 T:HIS103 4.4 16.1 1.0
ND1 T:HIS105 4.5 16.3 1.0
CG T:HIS103 4.5 16.4 1.0

Manganese binding site 6 out of 7 in 4ggf

Go back to Manganese Binding Sites List in 4ggf
Manganese binding site 6 out of 7 in the Crystal Structure of MN2+ Bound Calprotectin


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 MN2+ Bound Calprotectin within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mn202

b:24.9
occ:0.49
 OD1 T:ASP30 1.8 23.9 0.5
OD1 T:ASP30 1.8 22.7 0.5
NE2 S:HIS87 2.0 23.5 1.0
NE2 S:HIS83 2.1 21.8 1.0
NE2 T:HIS20 2.3 17.4 1.0
CG T:ASP30 2.3 24.0 0.5
OD2 T:ASP30 2.4 24.5 0.5
CG T:ASP30 2.7 23.9 0.5
CD2 S:HIS87 3.0 23.5 1.0
O T:HOH370 3.0 35.7 1.0
CD2 S:HIS83 3.0 20.5 1.0
CE1 S:HIS87 3.0 23.6 1.0
CE1 S:HIS83 3.1 21.7 1.0
CD2 T:HIS20 3.2 16.9 1.0
OD2 T:ASP30 3.2 24.4 0.5
CE1 T:HIS20 3.3 16.9 1.0
CB T:ASP30 3.8 24.1 0.5
CB T:ASP30 3.9 23.9 0.5
ND1 S:HIS87 4.1 23.6 1.0
CG S:HIS87 4.1 24.1 1.0
CG S:HIS83 4.1 19.8 1.0
ND1 S:HIS83 4.1 20.6 1.0
CG T:HIS20 4.4 16.3 1.0
ND1 T:HIS20 4.4 16.5 1.0
CA T:ASP30 4.5 22.6 0.5
CA T:ASP30 4.5 22.8 0.5
CE1 T:PHE19 4.5 17.9 1.0
OG S:SER86 4.7 21.0 1.0
O T:ASP30 4.8 22.3 0.5
O T:ASP30 4.8 22.2 0.5
O S:HIS83 4.9 20.2 1.0
O T:HOH301 4.9 23.1 1.0
CD1 T:PHE19 4.9 17.1 1.0

Manganese binding site 7 out of 7 in 4ggf

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Manganese binding site 7 out of 7 in the Crystal Structure of MN2+ Bound Calprotectin


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 MN2+ Bound Calprotectin within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mn201

b:23.7
occ:1.00
 NE2 V:HIS103 2.3 25.6 1.0
NE2 U:HIS27 2.3 22.2 1.0
NE2 V:HIS91 2.3 24.5 1.0
NE2 V:HIS95 2.3 27.1 1.0
NE2 V:HIS105 2.4 33.7 1.0
NE2 U:HIS17 2.4 28.0 1.0
CD2 V:HIS105 3.2 36.7 1.0
CE1 U:HIS17 3.2 28.4 1.0
CE1 V:HIS103 3.2 28.2 1.0
CD2 V:HIS103 3.2 27.6 1.0
CD2 U:HIS27 3.3 21.1 1.0
CE1 V:HIS95 3.3 26.8 1.0
CE1 U:HIS27 3.3 21.9 1.0
CE1 V:HIS91 3.3 24.5 1.0
CD2 V:HIS91 3.3 25.1 1.0
CD2 V:HIS95 3.3 27.7 1.0
CD2 U:HIS17 3.4 28.1 1.0
CE1 V:HIS105 3.4 31.0 1.0
ND1 U:HIS17 4.3 26.6 1.0
ND1 V:HIS103 4.4 28.4 1.0
CG U:HIS17 4.4 27.5 1.0
ND1 U:HIS27 4.4 21.6 1.0
CG V:HIS105 4.4 38.0 1.0
CG V:HIS103 4.4 28.6 1.0
ND1 V:HIS95 4.4 27.6 1.0
CG U:HIS27 4.5 20.2 1.0
ND1 V:HIS91 4.5 23.8 1.0
ND1 V:HIS105 4.5 33.7 1.0
CG V:HIS91 4.5 25.5 1.0
CG V:HIS95 4.5 30.6 1.0

Reference:

S.M.Damo, T.E.Kehl-Fie, N.Sugitani, M.E.Holt, S.Rathi, W.J.Murphy, Y.Zhang, C.Betz, L.Hench, G.Fritz, E.P.Skaar, W.J.Chazin. Molecular Basis For Manganese Sequestration By Calprotectin and Roles in the Innate Immune Response to Invading Bacterial Pathogens. Proc.Natl.Acad.Sci.Usa V. 110 3841 2013.
ISSN: ISSN 0027-8424
PubMed: 23431180
DOI: 10.1073/PNAS.1220341110
Page generated: Sat Oct 5 19:30:09 2024

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